diff --git a/.flake8 b/.flake8 index 7b2865c1..88077af0 100644 --- a/.flake8 +++ b/.flake8 @@ -6,7 +6,7 @@ exclude = __pycache__, build, dist, - doc/source/conf.py + docs/source/conf.py max-line-length = 79 # Ignore some style 'errors' produced while formatting by 'black' # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md index 6107962c..56bcd015 100644 --- a/.github/ISSUE_TEMPLATE/release_checklist.md +++ b/.github/ISSUE_TEMPLATE/release_checklist.md @@ -34,7 +34,7 @@ Please let the maintainer know that all checks are done and the package is ready - [ ] Ensure that the full release has appeared on PyPI successfully. -- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock. +- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock. - [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions. - [ ] Tag the maintainer for conda-forge release. diff --git a/.github/workflows/build-wheel-release-upload.yml b/.github/workflows/build-wheel-release-upload.yml index 485aa356..e40144a7 100644 --- a/.github/workflows/build-wheel-release-upload.yml +++ b/.github/workflows/build-wheel-release-upload.yml @@ -7,7 +7,7 @@ on: - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml jobs: - release: + build-release: uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0 with: project: diffpy.utils diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0e4a84d1..c424bcf7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ ci: submodules: false repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v6.0.0 hooks: - id: check-yaml - id: end-of-file-fixer @@ -21,45 +21,45 @@ repos: - id: check-toml - id: check-added-large-files - repo: https://github.com/psf/black - rev: 24.4.2 + rev: 26.5.1 hooks: - id: black - repo: https://github.com/pycqa/flake8 - rev: 7.0.0 + rev: 7.3.0 hooks: - id: flake8 - repo: https://github.com/pycqa/isort - rev: 5.13.2 + rev: 9.0.0a3 hooks: - id: isort args: ["--profile", "black"] - repo: https://github.com/kynan/nbstripout - rev: 0.7.1 + rev: 0.9.1 hooks: - id: nbstripout - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v6.0.0 hooks: - id: no-commit-to-branch name: Prevent Commit to Main Branch args: ["--branch", "main"] stages: [pre-commit] - repo: https://github.com/codespell-project/codespell - rev: v2.3.0 + rev: v2.4.2 hooks: - id: codespell additional_dependencies: - tomli # prettier - multi formatter for .json, .yml, and .md files - repo: https://github.com/pre-commit/mirrors-prettier - rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8 + rev: v4.0.0-alpha.8 hooks: - id: prettier additional_dependencies: - "prettier@^3.2.4" # docformatter - PEP 257 compliant docstring formatter - - repo: https://github.com/s-weigand/docformatter - rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c + - repo: https://github.com/PyCQA/docformatter + rev: v1.7.8 hooks: - id: docformatter additional_dependencies: [tomli] diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 47f7a017..aaa88895 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,4 +10,4 @@ python: - requirements: requirements/docs.txt sphinx: - configuration: doc/source/conf.py + configuration: docs/source/conf.py diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 48c7a51e..31873450 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,6 +4,70 @@ Release notes .. current developments +3.7.2 +===== + +**Added:** + +* Added Support for Python 3.10 + + +3.7.1 +===== + +**Added:** + +* Add support for python 3.11 for deprecator usage. + + +3.7.0 +===== + +**Added:** + +* Add ``build_deprecation_message`` helper for printing consistent deprecation messages. +* Add ``generate_deprecation_docstring`` for generating a template docstring for deprecated functions. +* Support for Python 3.14 +* Add ``@deprecated`` decorator. +* Add documentation for calculation mu. + +**Changed:** + +* load_data now takes a Path or a string for the file-path + +**Deprecated:** + +* diffpy.utils.parsers.loaddata.loadData replaced by diffpy.utils.parsers.load_data + +**Fixed:** + +* Normalize paths before assert in `test_serialization/test_load_multiple` to prevent possible Windows short/long name mismatch. +* All references to ``loadData`` changed to ``load_data`` due to that deprecation + +**Removed:** + +* Removed API that calculates mu from packing fraction. +* Support for Python 3.11 + + +3.6.1 +===== + +**Added:** + +* update isort, flake8 and black to set line limit to 79 + +**Fixed:** + +* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/). +* Update github CI to scikit-package standard +* Let ``DiffractionObject.get_array_index`` to use the ``xtype`` from its inputs. + +**Removed:** + +* Extra line break in each news after 3.6.0 in `CHANGELOG.rst` so that this rst can be rendered correctly when deployed + + 3.6.0 ===== diff --git a/CODE_OF_CONDUCT.rst b/CODE-OF-CONDUCT.rst similarity index 100% rename from CODE_OF_CONDUCT.rst rename to CODE-OF-CONDUCT.rst diff --git a/README.rst b/README.rst index 5fb8421e..388598b2 100644 --- a/README.rst +++ b/README.rst @@ -25,6 +25,7 @@ :target: https://anaconda.org/conda-forge/diffpy.utils .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff + :target: https://github.com/diffpy/diffpy.utils/pulls .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.utils :target: https://pypi.org/project/diffpy.utils/ @@ -35,8 +36,7 @@ .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue :target: https://github.com/diffpy/diffpy.utils/issues -diffpy.utils Package -======================================================================== +Shared utilities for diffpy packages. General utilities for analyzing diffraction data @@ -136,7 +136,7 @@ trying to commit again. Improvements and fixes are always appreciated. -Before contributing, please read our `Code of Conduct `_. +Before contributing, please read our `Code of Conduct `_. Contact ------- diff --git a/cookiecutter.json b/cookiecutter.json new file mode 100644 index 00000000..30db1791 --- /dev/null +++ b/cookiecutter.json @@ -0,0 +1,18 @@ +{ + "maintainer_name": "Simon Billinge", + "maintainer_email": "sb2896@columbia.edu", + "maintainer_github_username": "sbillinge", + "contributors": "Timur Davis, Chris Farrow, Pavol Juhas", + "license_holders": "The Trustees of Columbia University in the City of New York", + "project_name": "diffpy.utils", + "github_username_or_orgname": "diffpy", + "github_repo_name": "diffpy.utils", + "conda_pypi_package_dist_name": "diffpy.utils", + "package_dir_name": "diffpy.utils", + "project_short_description": "Shared utilities for diffpy packages.", + "project_keywords": "text data parsers, wx grid, diffraction objects", + "minimum_supported_python_version": "3.11", + "maximum_supported_python_version": "3.13", + "project_needs_c_code_compiled": "No", + "project_has_gui_tests": "No" +} diff --git a/doc/Makefile b/docs/Makefile similarity index 100% rename from doc/Makefile rename to docs/Makefile diff --git a/doc/make.bat b/docs/make.bat similarity index 100% rename from doc/make.bat rename to docs/make.bat diff --git a/doc/source/_static/.placeholder b/docs/source/_static/.placeholder similarity index 100% rename from doc/source/_static/.placeholder rename to docs/source/_static/.placeholder diff --git a/doc/source/api/diffpy.utils.parsers.rst b/docs/source/api/diffpy.utils.parsers.rst similarity index 100% rename from doc/source/api/diffpy.utils.parsers.rst rename to docs/source/api/diffpy.utils.parsers.rst diff --git a/doc/source/api/diffpy.utils.rst b/docs/source/api/diffpy.utils.rst similarity index 83% rename from doc/source/api/diffpy.utils.rst rename to docs/source/api/diffpy.utils.rst index e4de1d4f..a49f55b2 100644 --- a/doc/source/api/diffpy.utils.rst +++ b/docs/source/api/diffpy.utils.rst @@ -20,6 +20,14 @@ Subpackages Submodules ---------- +diffpy.utils.utils_app module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.utils.utils_app + :members: + :undoc-members: + :show-inheritance: + diffpy.utils.transforms module ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -44,10 +52,10 @@ diffpy.utils.tools module :undoc-members: :show-inheritance: -diffpy.utils.user_config module +diffpy.utils._deprecator module ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.utils.user_config +.. automodule:: diffpy.utils._deprecator :members: :undoc-members: :show-inheritance: diff --git a/doc/source/api/diffpy.utils.wx.rst b/docs/source/api/diffpy.utils.wx.rst similarity index 100% rename from doc/source/api/diffpy.utils.wx.rst rename to docs/source/api/diffpy.utils.wx.rst diff --git a/doc/source/conf.py b/docs/source/conf.py similarity index 99% rename from doc/source/conf.py rename to docs/source/conf.py index ae2443a1..6a8add42 100644 --- a/doc/source/conf.py +++ b/docs/source/conf.py @@ -140,7 +140,7 @@ "github_user": "diffpy", "github_repo": "diffpy.utils", "github_version": "main", - "conf_py_path": "/doc/source/", + "conf_py_path": "/docs/source/", } # Theme options are theme-specific and customize the look and feel of a theme @@ -223,7 +223,7 @@ # Output file base name for HTML help builder. basename = "diffpy.utils".replace(" ", "").replace(".", "") -htmlhelp_basename = basename + "doc" +htmlhelp_basename = basename + "docs" # -- Options for LaTeX output --------------------------------------------- diff --git a/doc/source/examples/diffraction_objects_example.rst b/docs/source/examples/diffraction_objects_example.rst similarity index 91% rename from doc/source/examples/diffraction_objects_example.rst rename to docs/source/examples/diffraction_objects_example.rst index 1122bf21..14c44c01 100644 --- a/doc/source/examples/diffraction_objects_example.rst +++ b/docs/source/examples/diffraction_objects_example.rst @@ -75,14 +75,19 @@ i.e., This makes it very easy to compare a diffraction pattern that was measured or calculated on one ``xtype`` with one that was measured or calculated on another. E.g., suppose that you have a calculated powder pattern from a CIF file that was calculated on a d-spacing grid using -some software package, and -you want to know if a diffraction pattern you have measured on a Q-grid is the same material. +some software package, which you could find in the example data folder called `CeO2_dspacing.xy` and +you want to know if a diffraction pattern you have measured on a Q-grid, where the example data is also +in the example data folder called `CeO2_mean_q.chi`, is the same material. You could simply load them both as diffraction objects and plot them together on the same grid. +Here the `xcalc` is the first column in the `CeO2_dspacing.xy` and `ycalc` is the second column in the same +file. Similarly, `xmeas` corresponds to the first column in the `CeO2_mean_q.chi` and `ymeas` is the second column in +the same file. .. code-block:: python calculated = DiffractionObject(xcalc, ycalc, "d") - measured = DiffractionObject(xmeas, ymeas, "tth", wavelength=0.717) + measured = DiffractionObject(xmeas, + ymeas, "q", wavelength=0.1) plt.plot(calculated.on_q()[0], calculated.on_q()[1]) plt.plot(measured.on_q()[0], measured.on_q()[1]) plt.show() @@ -180,7 +185,7 @@ For example, attempting to add a diffraction object and a string will raise an e .. code-block:: python - tth_ninety_index = diff_object1.get_array_index(90, xtype="tth") + tth_ninety_index = diff_object1.get_array_index(xvalue=90, xtype="tth") intensity_at_ninety = diff_object1.on_tth()[1][tth_ninety_index] If you do not specify an ``xtype``, it will default to the ``xtype`` used when creating the ``DiffractionObject``. @@ -190,8 +195,8 @@ you can find its closest index for ``q=0.25`` by typing either of the following: .. code-block:: python print(do._input_xtype) # remind ourselves which array was input. prints "q" in this case. - index = do.get_array_index(0.25) # no xtype passed, defaults to do._input_xtype, or in this example, q - index = do.get_array_index(0.25, xtype="q") # explicitly choose an xtype to specify a value + index = do.get_array_index(xvalue=0.25) # no xtype passed, defaults to do._input_xtype, or in this example, q + index = do.get_array_index(xvalue=0.25, xtype="q") # explicitly choose an xtype to specify a value 5. The ``dump`` function saves the diffraction data and relevant information to an xy format file with headers (widely used chi format used, for example, by Fit2D and diffpy. These files can be read by ``LoadData()`` diff --git a/docs/source/examples/example_data/CeO2_635um_accum_0.xy b/docs/source/examples/example_data/CeO2_635um_accum_0.xy new file mode 100644 index 00000000..97b1f9ee --- /dev/null +++ b/docs/source/examples/example_data/CeO2_635um_accum_0.xy @@ -0,0 +1,5631 @@ +2.00009989738464 22.6381633008874 +2.02462468668818 21.8208275836126 +2.04914947599173 21.0965692433941 +2.07367426529527 20.3054115384164 +2.09819905459881 19.2641083826002 +2.12272384390235 18.4351379931934 +2.14724863320589 18.0337418046386 +2.17177342250943 17.0477033414494 +2.19629821181297 16.5503211078054 +2.22082300111651 15.5206526241212 +2.24534779042006 15.439209919197 +2.2698725797236 14.7847596117706 +2.29439736902714 14.2088433412354 +2.31892215833068 13.6329270707001 +2.34344694763422 12.7806873370293 +2.36797173693776 12.3618391402764 +2.3924965262413 12.2076797345271 +2.41702131554484 11.7393841812131 +2.44154610484838 11.0965685459187 +2.46607089415193 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doc/source/examples/examples.rst rename to docs/source/examples/examples.rst index 5a30d3b4..f0cd8cae 100644 --- a/doc/source/examples/examples.rst +++ b/docs/source/examples/examples.rst @@ -12,3 +12,4 @@ Landing page for diffpy.utils examples. resample_example parsers_example tools_example + mu_calc_examples diff --git a/docs/source/examples/mu_calc_examples.rst b/docs/source/examples/mu_calc_examples.rst new file mode 100644 index 00000000..2326a46b --- /dev/null +++ b/docs/source/examples/mu_calc_examples.rst @@ -0,0 +1,123 @@ +.. _mu calc Example: + +:tocdepth: -1 + +Linear Absorption Coefficient (μ) Examples +######################################### + +These examples will demonstrate how to calculate the Linear absorption +coefficient, μ, using different methods provided in ``diffpy.utils``. + + +.. admonition:: Methods for obtaining linear absorption coefficient + + Obtaining μ can be done in **two + different ways** using ``diffpy.utils``. + + 1. **Using a "z-scan" measurement**: Perform a z-scan measurement + on the sample and use ``diffpy.utils.tools.compute_mud`` to calculate + μ. + 2. **Using tabulated values**: Given composition, density, and X-ray energy, + use ``diffpy.utils.tools.compute_mu_using_xraydb`` to calculate μ from + tabulated values. + +Why is μ Important? +----------------------- + +The linear absorption coefficient, μ, quantifies how much X-ray +radiation is absorbed by a material per unit length. It is a critical +parameter in many scientific techniques. + +For example, when calculating pair distribution functions (PDFs) +using ``diffpy.pdfgetx``, +a key assumption is that the linear absorption is negligible. +This is frequently the case for high-energy X-rays. However, +this must be corrected for when using low energy X-rays, such +as those from a laboratory source. To correct for linear absorption, +the linear absorption coefficient, μ, must be known. + +.. admonition:: Correcting for linear absorption with ``diffpy.labpdfproc`` + + If your objective is to correct for linear absorption in PDF calculations, + please refer to our package ``diffpy.labpdfproc``. This package is specifically + designed to correct your laboratory X-ray PDF data for absorption effects. + More information can be found in the + `diffpy.labpdfproc documentation `_. + + +Calculating μ from a "z-scan" Measurement +----------------------------------------- + +.. note:: + + The data we will be using for this example can be found, + `here `_. + +A "z-scan" measurement is the measured transmission of your X-ray incident beam +as a function of sample position. This is obtained by moving the sample +perpendicular to the X-ray beam (z-direction) and recording the transmitted +intensity at each position. This measured data looks something like this, + +.. image:: ../img/zscan-plot.png + :alt: Example of a z-scan measurement. + :align: center + :width: 300px + +Using this z-scan data, you can calculate **μ·d**, where d is the inner diameter of +your sample capillary. To do this, simply pass your z-scan measurement to the ``compute_mud`` +function from the ``diffpy.utils.tools`` module. + + +First, import the ``compute_mud`` function, + +.. code-block:: python + + from diffpy.utils.tools import compute_mud + +Next, pass the filepath to the function, + +.. code-block:: python + + filepath = "CeO2_635um_zscan_200umSlit_chanClose_exported.xy" + capillary_diameter = 0.5 # mm + mud = compute_mud(filepath) + print(f"Calculated mu*d: {round(mud, 3)}") + print(f"Calculated mu: {round(mud / capillary_diameter, 3)} mm^-1") + +This will output the calculated value of μ·d, which is unitless, and μ in mm\ :sup:`-1`. + +.. code-block:: console + + Calculated mu*d: 3.489 + Calculated mu: 6.977 mm^-1 + +Calculating μ from Tabulated Values +----------------------------------- + +The function to calculate μ from tabulated values is located +in the ``diffpy.utils.tools`` module. So first, import the function, + +.. code-block:: python + + from diffpy.utils.tools import compute_mu_using_xraydb + +To calculate μ, you need to know the sample composition, and X-ray energy, and sample mass density (g/cm\ :sup:`3`). + +.. code-block:: python + + composition = "Fe2O3" + energy_keV = 17.45 # Mo K-alpha energy + sample_mass_density = 5.24 # g/cm^3 + +Now calculate μ using the ``compute_mu_using_xraydb`` function. + +.. code-block:: python + + mu = compute_mu_using_xraydb(composition, energy_keV, sample_mass_density) + print(f"Calculated mu: {round(mu, 3)} mm^-1") + +This will output the calculated linear absorption coefficient, μ, in mm\ :sup:`-1`. + +.. code-block:: console + + Calculated mu: 13.967 mm^-1 diff --git a/doc/source/examples/parsers_example.rst b/docs/source/examples/parsers_example.rst similarity index 80% rename from doc/source/examples/parsers_example.rst rename to docs/source/examples/parsers_example.rst index 92135f3b..747d0c4f 100644 --- a/doc/source/examples/parsers_example.rst +++ b/docs/source/examples/parsers_example.rst @@ -13,13 +13,13 @@ Using the parsers module, we can load file data into simple and easy-to-work-wit Our goal will be to extract the data, and the parameters listed in the header, from this file and load it into our program. -2) To get the data table, we will use the ``loadData`` function. The default behavior of this +2) To get the data table, we will use the ``load_data`` function. The default behavior of this function is to find and extract a data table from a file. .. code-block:: python - from diffpy.utils.parsers.loaddata import loadData - data_table = loadData('') + from diffpy.utils.parsers import load_data + data_table = load_data('') While this will work with most datasets, on our ``data.txt`` file, we got a ``ValueError``. The reason for this is due to the comments ``$ Phase Transition Near This Temperature Range`` and ``--> Note Significant Jump in Rw <--`` @@ -27,9 +27,9 @@ embedded within the dataset. To fix this, try using the ``comments`` parameter. .. code-block:: python - data_table = loadData('', comments=['$', '-->']) + data_table = load_data('', comments=['$', '-->']) -This parameter tells ``loadData`` that any lines beginning with ``$`` and ``-->`` are just comments and +This parameter tells ``load_data`` that any lines beginning with ``$`` and ``-->`` are just comments and more entries in our data table may follow. Here are a few other parameters to test out: @@ -39,7 +39,7 @@ Here are a few other parameters to test out: .. code-block:: python - loadData('', comments=['$', '-->'], delimiter=',') + load_data('', comments=['$', '-->'], delimiter=',') returns an empty list. * ``minrows=50``: Only look for data tables with at least 50 rows. Since our data table has much less than that many @@ -47,7 +47,7 @@ returns an empty list. .. code-block:: python - loadData('', comments=['$', '-->'], minrows=50) + load_data('', comments=['$', '-->'], minrows=50) returns an empty list. * ``usecols=[0, 3]``: Only return the 0th and 3rd columns (zero-indexed) of the data table. For ``data.txt``, this @@ -55,21 +55,21 @@ returns an empty list. .. code-block:: python - loadData('', comments=['$', '-->'], usecols=[0, 3]) + load_data('', comments=['$', '-->'], usecols=[0, 3]) -3) Next, to get the header information, we can again use ``loadData``, +3) Next, to get the header information, we can again use ``load_data``, but this time with the ``headers`` parameter enabled. .. code-block:: python - hdata = loadData('', comments=['$', '-->'], headers=True) + hdata = load_data('', comments=['$', '-->'], headers=True) 4) Rather than working with separate ``data_table`` and ``hdata`` objects, it may be easier to combine them into a single dictionary. We can do so using the ``serialize_data`` function. .. code-block:: python - from diffpy.utils.parsers.loaddata import serialize_data + from diffpy.utils.parsers.serialization import serialize_data file_data = serialize_data('', hdata, data_table, serial_file='') - The returned value, ``parsed_file_data``, is the dictionary we just added to ``serialfile.json``. - To extract the data from the serial file, we use ``deserialize_data``. +The returned value, ``parsed_file_data``, is the dictionary we just added to ``serialfile.json``. To extract the data from the serial file, we use ``deserialize_data``. .. code-block:: python @@ -117,8 +116,8 @@ Now we can extract specific data table columns from the dictionary. .. code-block:: python - data_table = loadData('') - hdata = loadData('', headers=True) + data_table = load_data('') + hdata = load_data('', headers=True) serialize_data('', hdata, data_table, serial_file='') The serial file ``serialfile.json`` should now contain two entries: ``data.txt`` and ``moredata.txt``. diff --git a/doc/source/examples/resample_example.rst b/docs/source/examples/resample_example.rst similarity index 85% rename from doc/source/examples/resample_example.rst rename to docs/source/examples/resample_example.rst index 4884f5c9..32e3e02a 100644 --- a/doc/source/examples/resample_example.rst +++ b/docs/source/examples/resample_example.rst @@ -16,25 +16,13 @@ given enough datapoints. .. code-block:: python - from diffpy.utils.parsers.loaddata import loadData - nickel_datatable = loadData('') - nitarget_datatable = loadData('') + from diffpy.utils.parsers import load_data + nickel_datatable = load_data('') + nitarget_datatable = load_data('') Each data table has two columns: first is the grid and second is the function value. To extract the columns, we can utilize the serialize function ... -.. code-block:: python - - from diffpy.utils.parsers.serialization import serialize_data - nickel_data = serialize_data('Nickel.gr', {}, nickel_datatable, dt_colnames=['grid', 'func']) - nickel_grid = nickel_data['Nickel.gr']['grid'] - nickel_func = nickel_data['Nickel.gr']['func'] - target_data = serialize_data('NiTarget.gr', {}, nitarget_datatable, dt_colnames=['grid', 'function']) - target_grid = nickel_data['Nickel.gr']['grid'] - target_func = nickel_data['Nickel.gr']['func'] - -To extract the columns, we can utilize the serialize function ... - .. code-block:: python from diffpy.utils.parsers.serialization import serialize_data diff --git a/doc/source/examples/tools_example.rst b/docs/source/examples/tools_example.rst similarity index 100% rename from doc/source/examples/tools_example.rst rename to docs/source/examples/tools_example.rst diff --git a/doc/source/examples/transforms_example.rst b/docs/source/examples/transforms_example.rst similarity index 97% rename from doc/source/examples/transforms_example.rst rename to docs/source/examples/transforms_example.rst index 2fc40c4a..70d63fb4 100644 --- a/doc/source/examples/transforms_example.rst +++ b/docs/source/examples/transforms_example.rst @@ -59,5 +59,5 @@ This example will demonstrate how to use the functions in the from diffpy.utils.transforms import d_to_tth wavelength = 0.71 - d = np.array([1.0, 0.8, 0.6, 0.4, 0.2]) + d = np.array([1.0, 0.8, 0.6, 0.4]) tth = d_to_tth(d, wavelength) diff --git a/docs/source/img/zscan-plot.png b/docs/source/img/zscan-plot.png new file mode 100644 index 00000000..f0cc9ade Binary files /dev/null and b/docs/source/img/zscan-plot.png differ diff --git a/doc/source/index.rst b/docs/source/index.rst similarity index 96% rename from doc/source/index.rst rename to docs/source/index.rst index a406daa3..27359a3f 100644 --- a/doc/source/index.rst +++ b/docs/source/index.rst @@ -6,7 +6,7 @@ diffpy.utils - General utilities for analyzing diffraction data -| Software version |release|. +| Software version |release| | Last updated |today|. The diffpy.utils package provides a number of functions and classes designed to help @@ -33,7 +33,7 @@ Illustrations of when and how one would use various diffpy.utils functions. Authors ======= -diffpy.utils is developed by members of the Billinge Group at +``diffpy.utils`` is developed by members of the Billinge Group at Columbia University and at Brookhaven National Laboratory including Pavol Juhás, Christopher L. Farrow, Simon J. L. Billinge, Andrew Yang, with contributions from many Billinge Group members and diff --git a/doc/source/license.rst b/docs/source/license.rst similarity index 100% rename from doc/source/license.rst rename to docs/source/license.rst diff --git a/doc/source/release.rst b/docs/source/release.rst similarity index 100% rename from doc/source/release.rst rename to docs/source/release.rst diff --git a/doc/source/utilities/diffraction_objects_utility.rst b/docs/source/utilities/diffraction_objects_utility.rst similarity index 100% rename from doc/source/utilities/diffraction_objects_utility.rst rename to docs/source/utilities/diffraction_objects_utility.rst diff --git a/doc/source/utilities/parsers_utility.rst b/docs/source/utilities/parsers_utility.rst similarity index 85% rename from doc/source/utilities/parsers_utility.rst rename to docs/source/utilities/parsers_utility.rst index ffaf768e..954405b5 100644 --- a/doc/source/utilities/parsers_utility.rst +++ b/docs/source/utilities/parsers_utility.rst @@ -5,7 +5,7 @@ Parsers Utility The ``diffpy.utils.parsers`` module allows users to easily and robustly load file data into a Python project. -- ``loaddata.loadData()``: Find and load a data table/block from a text file. This seems to work for most datafiles +- ``loaddata.load_data()``: Find and load a data table/block from a text file. This seems to work for most datafiles including those generated by diffpy programs. Running only ``numpy.loadtxt`` will result in errors for most these files as there is often excess data or parameters stored above the data block. Users can instead choose to load all the parameters of the form `` = `` into a dictionary @@ -17,7 +17,7 @@ The ``diffpy.utils.parsers`` module allows users to easily and robustly load fil - ``serialization.deserialize_data()``: Load data from a serial file format into a Python dictionary. Currently, the only supported serial format is ``.json``. -- ``serialization.serialize_data()``: Serialize the data generated by ``loadData()`` into a serial file format. Currently, the only +- ``serialization.serialize_data()``: Serialize the data generated by ``load_data()`` into a serial file format. Currently, the only supported serial format is ``.json``. For a more in-depth tutorial for how to use these parser utilities, click :ref:`here `. diff --git a/doc/source/utilities/resample_utility.rst b/docs/source/utilities/resample_utility.rst similarity index 100% rename from doc/source/utilities/resample_utility.rst rename to docs/source/utilities/resample_utility.rst diff --git a/doc/source/utilities/tools_utility.rst b/docs/source/utilities/tools_utility.rst similarity index 100% rename from doc/source/utilities/tools_utility.rst rename to docs/source/utilities/tools_utility.rst diff --git a/doc/source/utilities/transforms_utility.rst b/docs/source/utilities/transforms_utility.rst similarity index 100% rename from doc/source/utilities/transforms_utility.rst rename to docs/source/utilities/transforms_utility.rst diff --git a/doc/source/utilities/utilities.rst b/docs/source/utilities/utilities.rst similarity index 100% rename from doc/source/utilities/utilities.rst rename to docs/source/utilities/utilities.rst diff --git a/news/changelog-3.6.0-line-break.rst b/news/changelog-3.6.0-line-break.rst deleted file mode 100644 index ac80a0a1..00000000 --- a/news/changelog-3.6.0-line-break.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* Extra line break in each news after 3.6.0 in `CHANGELOG.rst` so that this rst can be rendered correctly when deployed - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/readme.rst b/news/dependency-update.rst similarity index 67% rename from news/readme.rst rename to news/dependency-update.rst index 978de17c..abd1d67a 100644 --- a/news/readme.rst +++ b/news/dependency-update.rst @@ -1,6 +1,6 @@ **Added:** -* no news needed: just a chore of no import +* No news needed: updating docformatter, isort and black. Not user facing. **Changed:** diff --git a/news/doc-migration.rst b/news/doc-migration.rst deleted file mode 100644 index b0ec659f..00000000 --- a/news/doc-migration.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/). - -**Security:** - -* diff --git a/news/linelength79.rst b/news/linelength79.rst deleted file mode 100644 index be12d2fb..00000000 --- a/news/linelength79.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* update isort, flake8 and black to set line limit to 79 - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/news-and-misc.rst b/news/news-and-misc.rst deleted file mode 100644 index 339e8df3..00000000 --- a/news/news-and-misc.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* No news item needed, bringing package up to ``scikit-package 5v0.1.0`` standards. - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* - -**Security:** - -* diff --git a/news/setup-CI.rst b/news/setup-CI.rst deleted file mode 100644 index bf692d68..00000000 --- a/news/setup-CI.rst +++ /dev/null @@ -1,23 +0,0 @@ -**Added:** - -* - -**Changed:** - -* - -**Deprecated:** - -* - -**Removed:** - -* - -**Fixed:** - -* Update github CI to scikit-package standard - -**Security:** - -* diff --git a/pyproject.toml b/pyproject.toml index ef9192f4..ec8ad217 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ maintainers = [ description = "General utilities for analyzing diffraction data" keywords = ['text data parsers', 'wx grid', 'diffraction objects'] readme = "README.rst" -requires-python = ">=3.11, <3.14" +requires-python = ">=3.10, <3.15" classifiers = [ 'Development Status :: 5 - Production/Stable', 'Environment :: Console', @@ -25,9 +25,11 @@ classifiers = [ 'Operating System :: Microsoft :: Windows', 'Operating System :: POSIX', 'Operating System :: Unix', + 'Programming Language :: Python :: 3.10', 'Programming Language :: Python :: 3.11', 'Programming Language :: Python :: 3.12', 'Programming Language :: Python :: 3.13', + 'Programming Language :: Python :: 3.14', 'Topic :: Scientific/Engineering :: Physics', 'Topic :: Scientific/Engineering :: Chemistry', ] @@ -48,6 +50,9 @@ include = ["*"] # package names should match these glob patterns (["*"] by defa exclude = [] # exclude packages matching these glob patterns (empty by default) namespaces = false # to disable scanning PEP 420 namespaces (true by default) +[project.scripts] +diffpy-utils = "diffpy.utils_app:main" + [tool.setuptools.dynamic] dependencies = {file = ["requirements/pip.txt"]} @@ -56,6 +61,11 @@ exclude-file = ".codespell/ignore_lines.txt" ignore-words = ".codespell/ignore_words.txt" skip = "*.cif,*.dat" +[tool.docformatter] +recursive = true +wrap-summaries = 72 +wrap-descriptions = 72 + [tool.black] line-length = 79 include = '\.pyi?$' diff --git a/requirements/test.txt b/requirements/tests.txt similarity index 100% rename from requirements/test.txt rename to requirements/tests.txt diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py index 00208e23..99124eeb 100644 --- a/src/diffpy/__init__.py +++ b/src/diffpy/__init__.py @@ -21,7 +21,6 @@ Blank namespace package. """ - from pkgutil import extend_path __path__ = extend_path(__path__, __name__) diff --git a/src/diffpy/utils/_deprecator.py b/src/diffpy/utils/_deprecator.py new file mode 100644 index 00000000..9a0347de --- /dev/null +++ b/src/diffpy/utils/_deprecator.py @@ -0,0 +1,178 @@ +import functools +import warnings + +# Deprecated decorator is available for Python 3.13+, once +# Support for earlier versions is dropped, this custom +# implementation can be removed. +try: + from warnings import deprecated as _builtin_deprecated +except ImportError: + _builtin_deprecated = None + + +def deprecated(message, *, category=DeprecationWarning, stacklevel=1): + """Deprecation decorator for functions and classes that is + compatible with Python versions prior to 3.13. + + Examples + -------- + Basic usage with a deprecated function: + + .. code-block:: python + + from diffpy.utils._deprecator import ( + deprecated, build_deprecation_message + ) + + deprecation_warning = build_deprecation_message("diffpy.utils", + "old_function", + "new_function", + "4.0.0") + + @deprecated(deprecation_warning) + def old_function(x, y): + '''This function is deprecated and will be removed in version + 4.0.0. Please use new_function instead''' + return new_function(x, y) + + def new_function(x, y): + return x + y + + old_function(1, 2) # Works but emits DeprecationWarning + new_function(1, 2) # Works, no warning + + + Deprecating a class: + + .. code-block:: python + + from diffpy.utils._deprecator import ( + deprecated, build_deprecation_message + ) + deprecation_warning = build_deprecation_message("diffpy.utils", + "OldAtom", + "NewAtom", + "4.0.0") + + @deprecated(deprecation_warning) + class OldAtom: + def __new__(cls, *args, **kwargs): + warnings.warn( + "OldAtom is deprecated and will be removed in + version 4.0.0. Use NewClass instead.", + DeprecationWarning, + stacklevel=2, + ) + return NewAtom(*args, **kwargs) + + class NewAtom: + def __init__(self, symbol): + self.symbol = symbol + + a = OldAtom("C") # Works but emits DeprecationWarning + b = NewAtom("C") # Works with no warning + """ + if _builtin_deprecated is not None: + return _builtin_deprecated( + message, category=category, stacklevel=stacklevel + ) + if not isinstance(message, str): + raise TypeError( + f"Expected an object of type str for 'message', not " + f"{type(message).__name__!r}" + ) + + def decorator(obj): + setattr(obj, "__deprecated__", message) + if callable(obj): + + @functools.wraps(obj) + def wrapper(*args, **kwargs): + warnings.warn(message, category, stacklevel=stacklevel + 1) + return obj(*args, **kwargs) + + return wrapper + raise TypeError( + "deprecated decorator can only be applied to functions or classes" + ) + + return decorator + + +def build_deprecation_message( + old_base, old_name, new_name, removal_version, new_base=None +): + """Generate a deprecation message. + + Parameters + ---------- + old_base : str + The base module or class where the deprecated item resides. + This will look like the import statement used in the code + currently + old_name : str + The name of the deprecated item. + new_name : str + The name of the new item to use. + removal_version : str + The version when the deprecated item will be removed. + new_base : str Optional. Defaults to old_base. + The base module or class where the new item resides. + This will look like the import statement that + will be used in the code moving forward. If not specified, + the new base defaults to the old one. + + Returns + ------- + str + A formatted deprecation message. + """ + if new_base is None: + new_base = old_base + return ( + f"'{old_base}.{old_name}' is deprecated and will be removed in " + f"version {removal_version}. Please use '{new_base}.{new_name}' " + f"instead." + ) + + +def generate_deprecation_docstring(new_name, removal_version, new_base=None): + """Generate a docstring for copy-pasting into a deprecated function. + + This function will print the text to the terminal for copy-pasting. + + Parameters + ---------- + new_name : str + The name of the new function or class to replace the existing one. + removal_version : str + The version when the deprecated item is targeted for removal, + e.g., 4.0.0. + new_base : str, optional + The new base for importing. The new import statement would look like + "from new_base import new_name". Defaults to None. + + Example + ------- + >>> from diffpy.utils._deprecator import generate_deprecation_docstring + >>> generate_deprecation_docstring("new_name", "4.0.0") + + The message looks like: + This function has been deprecated and will be removed in version + {removal_version}. Please use {new_base}.{new_name} instead. + + + Returns + ------- + None + """ + if new_base is None: + function_location = new_name + else: + function_location = f"{new_base}.{new_name}" + print( + f"This function has been deprecated and will be removed in version " + f"{removal_version}.\n" + f"Please use {function_location} instead." + ) + return diff --git a/src/diffpy/utils/diffraction_objects.py b/src/diffpy/utils/diffraction_objects.py index 25f32f4d..aa58033f 100644 --- a/src/diffpy/utils/diffraction_objects.py +++ b/src/diffpy/utils/diffraction_objects.py @@ -108,18 +108,18 @@ def __init__( Parameters ---------- - xarray : ndarray + xarray : ``ndarray`` The independent variable array containing "q", "tth", or "d" values. - yarray : ndarray + yarray : ``ndarray`` The dependent variable array corresponding to intensity values. xtype : str The type of the independent variable in `xarray`. Must be one of {*XQUANTITIES}. - wavelength : float, optional, default is None. + wavelength : float, ``optional``, default is None. The wavelength of the incoming beam, specified in angstroms (Å) - scat_quantity : str, optional, default is an empty string "". + scat_quantity : str, ``optional``, default is an empty string "". The type of scattering experiment (e.g., "x-ray", "neutron"). - name : str, optional, default is an empty string "". + name : str, ``optional``, default is an empty string "". The name or label for the scattering data. metadata : dict, optional, default is an empty dictionary {} The additional metadata associated with the diffraction object. @@ -211,8 +211,8 @@ def __eq__(self, other): return True def __add__(self, other): - """Add a scalar value or another DiffractionObject to the yarray of the - DiffractionObject. + """Add a scalar value or another DiffractionObject to the yarray + of the DiffractionObject. Parameters ---------- @@ -262,8 +262,8 @@ def __add__(self, other): __radd__ = __add__ def __sub__(self, other): - """Subtract scalar value or another DiffractionObject to the yarray of - the DiffractionObject. + """Subtract scalar value or another DiffractionObject to the + yarray of the DiffractionObject. This method behaves similarly to the `__add__` method, but performs subtraction instead of addition. For details on parameters, returns @@ -290,8 +290,8 @@ def __sub__(self, other): __rsub__ = __sub__ def __mul__(self, other): - """Multiply a scalar value or another DiffractionObject with the yarray - of this DiffractionObject. + """Multiply a scalar value or another DiffractionObject with the + yarray of this DiffractionObject. This method behaves similarly to the `__add__` method, but performs multiplication instead of addition. For details on parameters, @@ -318,8 +318,8 @@ def __mul__(self, other): __rmul__ = __mul__ def __truediv__(self, other): - """Divide the yarray of this DiffractionObject by a scalar value or - another DiffractionObject. + """Divide the yarray of this DiffractionObject by a scalar value + or another DiffractionObject. This method behaves similarly to the `__add__` method, but performs division instead of addition. For details on parameters, returns, @@ -360,7 +360,7 @@ def all_arrays(self): Returns ------- - ndarray + ``ndarray`` The shape (len(data), 4) 2D array with columns containing the ` yarray` (intensity) and the `xarray` values in q, tth, and d. @@ -386,7 +386,7 @@ def input_xtype(self): Returns ------- input_xtype : str - The type of `xarray`, which must be one of {*XQUANTITIES}. + The type of `xarray`, which must be one of ``{*XQUANTITIES}``. """ return self._input_xtype @@ -400,7 +400,7 @@ def uuid(self): Returns ------- - uuid : UUID + uuid : ``UUID`` The unique identifier of the DiffractionObject instance. """ return self._uuid @@ -409,17 +409,17 @@ def uuid(self): def uuid(self, _): raise AttributeError(_setter_wmsg("uuid")) - def get_array_index(self, xtype, xvalue): - """Return the index of the closest value in the array associated with + def get_array_index(self, xvalue, xtype=None): + f"""Return the index of the closest value in the array associated with the specified xtype and the value provided. Parameters ---------- - xtype : str - The type of the independent variable in `xarray`. Must be one - of {*XQUANTITIES}. xvalue : float The value of the xtype to find the closest index for. + xtype : str, optional + The type of the independent variable in `xarray`. Must be one + of {*XQUANTITIES, }. Default is {self._input_xtype} Returns ------- @@ -427,8 +427,11 @@ def get_array_index(self, xtype, xvalue): The index of the closest value in the array associated with the specified xtype and the value provided. """ - - xtype = self._input_xtype + if xtype is None: + xtype = self._input_xtype + else: + if xtype not in XQUANTITIES: + raise ValueError(_xtype_wmsg(xtype)) xarray = self.on_xtype(xtype)[0] if len(xarray) == 0: raise ValueError( @@ -471,31 +474,34 @@ def _get_original_array(self): return self.on_d(), "d" def on_q(self): - """Return the tuple of two 1D numpy arrays containing q and y data. + """Return the tuple of two 1D numpy arrays containing q and y + data. Returns ------- - (q-array, y-array) : tuple of ndarray + (q-array, y-array) : tuple of ``ndarray`` The tuple containing two 1D numpy arrays with q and y data """ return [self.all_arrays[:, 1], self.all_arrays[:, 0]] def on_tth(self): - """Return the tuple of two 1D numpy arrays containing tth and y data. + """Return the tuple of two 1D numpy arrays containing tth and y + data. Returns ------- - (tth-array, y-array) : tuple of ndarray + (tth-array, y-array) : tuple of ``ndarray`` The tuple containing two 1D numpy arrays with tth and y data """ return [self.all_arrays[:, 2], self.all_arrays[:, 0]] def on_d(self): - """Return the tuple of two 1D numpy arrays containing d and y data. + """Return the tuple of two 1D numpy arrays containing d and y + data. Returns ------- - (d-array, y-array) : tuple of ndarray + (d-array, y-array) : tuple of ``ndarray`` The tuple containing two 1D numpy arrays with d and y data """ return [self.all_arrays[:, 3], self.all_arrays[:, 0]] @@ -503,8 +509,8 @@ def on_d(self): def scale_to( self, target_diff_object, q=None, tth=None, d=None, offset=None ): - """Return a new diffraction object which is the current object but - rescaled in y to the target. + """Return a new diffraction object which is the current object + but rescaled in y to the target. By default, if `q`, `tth`, or `d` are not provided, scaling is based on the max intensity from each object. Otherwise, y-value in @@ -519,12 +525,12 @@ def scale_to( target_diff_object: DiffractionObject The diffraction object you want to scale the current one onto. - q, tth, d : float, optional, default is None + q, tth, d : float, ``optional``, default is None The value of the x-array where you want the curves to line up vertically. Specify a value on one of the allowed grids, q, tth, or d), e.g., q=10. - offset : float, optional, default is None + offset : float, ``optional``, default is None The offset to add to the scaled y-values. Returns @@ -565,22 +571,23 @@ def scale_to( return scaled_do def on_xtype(self, xtype): - """Return a tuple of two 1D numpy arrays containing x and y data. + """Return a tuple of two 1D numpy arrays containing x and y + data. Parameters ---------- xtype : str The type of quantity for the independent variable chosen from - {*XQUANTITIES, } + ``{*XQUANTITIES, }`` Raises ------ ValueError - Raised when the specified xtype is not among {*XQUANTITIES, } + Raised when the specified xtype is not among ``{*XQUANTITIES, }`` Returns ------- - (xarray, yarray) : tuple of ndarray + (xarray, yarray) : tuple of ``ndarray`` The tuple containing two 1D numpy arrays with x and y data for the specified xtype. """ @@ -594,16 +601,17 @@ def on_xtype(self, xtype): raise ValueError(_xtype_wmsg(xtype)) def dump(self, filepath, xtype=None): - """Dump the xarray and yarray of the diffraction object to a two-column - file, with the associated information included in the header. + """Dump the xarray and yarray of the diffraction object to a + two-column file, with the associated information included in the + header. Parameters ---------- filepath : str The filepath where the diffraction object will be dumped - xtype : str, optional, default is q + xtype : str, ``optional``, default is q The type of quantity for the independent variable chosen from - {*XQUANTITIES, } + ``{*XQUANTITIES, }`` Examples -------- diff --git a/src/diffpy/utils/parsers/__init__.py b/src/diffpy/utils/parsers/__init__.py index a0278e27..956f2e6d 100644 --- a/src/diffpy/utils/parsers/__init__.py +++ b/src/diffpy/utils/parsers/__init__.py @@ -6,10 +6,18 @@ # (c) 2010 The Trustees of Columbia University # in the City of New York. All rights reserved. # -# File coded by: Chris Farrow +# File coded by: Simon Billinge # # See AUTHORS.txt for a list of people who contributed. # See LICENSE_DANSE.txt for license information. # ############################################################################## """Various utilities related to data parsing and manipulation.""" + +# this allows load_data to be imported from diffpy.utils.parsers +# it is needed during deprecation of the old loadData structure +# when we remove loadData we can move all the parser functionality +# a parsers.py module (like tools.py) and remove this if we want +from .loaddata import load_data + +__all__ = ["load_data"] diff --git a/src/diffpy/utils/parsers/loaddata.py b/src/diffpy/utils/parsers/loaddata.py index 05d37497..58a49a46 100644 --- a/src/diffpy/utils/parsers/loaddata.py +++ b/src/diffpy/utils/parsers/loaddata.py @@ -13,15 +13,205 @@ # ############################################################################## -import os +from pathlib import Path import numpy from diffpy.utils import validators +from diffpy.utils._deprecator import build_deprecation_message, deprecated +base = "diffpy.utils.parsers.loaddata" +removal_version = "4.0.0" +loaddata_deprecation_msg = build_deprecation_message( + base, + "loadData", + "load_data", + removal_version, + new_base="diffpy.utils.parsers", +) + + +@deprecated(loaddata_deprecation_msg) def loadData( filename, minrows=10, headers=False, hdel="=", hignore=None, **kwargs +): + """This function has been deprecated and will be removed in version + 4.0.0. + + Please use diffpy.utils.parsers.load_data instead. + """ + return load_data(filename, minrows, headers, hdel, hignore, **kwargs) + + +class TextDataLoader(object): + """Smart loading of a text data with possibly multiple datasets. + + Parameters + ---------- + minrows: int + Minimum number of rows in the first data block. (Default 10.) + usecols: tuple + Which columns in our dataset to use. Ignores all other columns. If + None (default), use all columns. + skiprows + Rows in dataset to skip. (Currently not functional.) + """ + + def __init__(self, minrows=10, usecols=None, skiprows=None): + if minrows is not None: + self.minrows = minrows + if usecols is not None: + self.usecols = tuple(usecols) + # FIXME: implement usage in _findDataBlocks + if skiprows is not None: + self.skiprows = skiprows + # data items + self._reset() + return + + def _reset(self): + self.filename = "" + self.headers = [] + self.datasets = [] + self._resetvars() + return + + def _resetvars(self): + self._filename = "" + self._lines = None + self._splitlines = None + self._words = None + self._linerecs = None + self._wordrecs = None + return + + def read(self, filename): + """Open a file and run readfp. + + Use if file is not already open for read byte. + """ + with open(filename, "rb") as fp: + self.readfp(fp) + return + + def readfp(self, fp, append=False): + """Get file details. + + File details include: + * File name. + * All data blocks findable by load_data. + * Headers (if present) for each data block. (Generally the headers + contain column name information). + """ + self._reset() + # try to read lines from fp first + self._lines = fp.readlines() + # and if good, assign filename + self.filename = getattr(fp, "name", "") + self._words = "".join(self._lines).split() + self._splitlines = [line.split() for line in self._lines] + self._findDataBlocks() + return + + def _findDataBlocks(self): + mincols = 1 + if self.usecols is not None and len(self.usecols): + mincols = max(mincols, max(self.usecols) + 1) + mincols = max(mincols, abs(min(self.usecols))) + nlines = len(self._lines) + nwords = len(self._words) + # idx - line index, nw0, nw1 - index of the first and last word, + # nf - number of words, ok - has data + self._linerecs = numpy.recarray( + (nlines,), + dtype=[ + ("idx", int), + ("nw0", int), + ("nw1", int), + ("nf", int), + ("ok", bool), + ], + ) + lr = self._linerecs + lr.idx = numpy.arange(nlines) + lr.nf = [len(sl) for sl in self._splitlines] + lr.nw1 = lr.nf.cumsum() + lr.nw0 = lr.nw1 - lr.nf + lr.ok = True + # word records + lw = self._wordrecs = numpy.recarray( + (nwords,), + dtype=[ + ("idx", int), + ("line", int), + ("col", int), + ("ok", bool), + ("value", float), + ], + ) + lw.idx = numpy.arange(nwords) + n1 = numpy.zeros(nwords, dtype=bool) + n1[lr.nw1[:-1]] = True + lw.line = n1.cumsum() + lw.col = lw.idx - lr.nw0[lw.line] + lw.ok = True + values = nwords * [0.0] + for i, w in enumerate(self._words): + try: + values[i] = float(w) + except ValueError: + lw.ok[i] = False + # prune lines that have a non-float values: + lw.values = values + if self.usecols is None: + badlines = lw.line[~lw.ok] + lr.ok[badlines] = False + else: + for col in self.usecols: + badlines = lw.line[(lw.col == col) & ~lw.ok] + lr.ok[badlines] = False + lr1 = lr[lr.nf >= mincols] + okb = numpy.r_[lr1.ok[:1], lr1.ok[1:] & ~lr1.ok[:-1], False] + oke = numpy.r_[False, ~lr1.ok[1:] & lr1.ok[:-1], lr1.ok[-1:]] + blockb = numpy.r_[True, lr1.nf[1:] != lr1.nf[:-1], False] + blocke = numpy.r_[False, blockb[1:-1], True] + beg = numpy.nonzero(okb | blockb)[0] + end = numpy.nonzero(oke | blocke)[0] + rowcounts = end - beg + assert not numpy.any(rowcounts < 0) + goodrows = rowcounts >= self.minrows + begend = numpy.transpose([beg, end - 1])[goodrows] + hbeg = 0 + for dbeg, dend in begend: + bb1 = lr1[dbeg] + ee1 = lr1[dend] + hend = bb1.idx + header = "".join(self._lines[hbeg:hend]) + hbeg = ee1.idx + 1 + if self.usecols is None: + data = numpy.reshape(lw.value[bb1.nw0 : ee1.nw1], (-1, bb1.nf)) + else: + tdata = numpy.empty( + (len(self.usecols), dend - dbeg), dtype=float + ) + for j, trow in zip(self.usecols, tdata): + j %= bb1.nf + trow[:] = lw.value[bb1.nw0 + j : ee1.nw1 : bb1.nf] + data = tdata.transpose() + self.headers.append(header) + self.datasets.append(data) + # finish reading to a last header and empty dataset + if hbeg < len(self._lines): + header = "".join(self._lines[hbeg:]) + data = numpy.empty(0, dtype=float) + self.headers.append(header) + self.datasets.append(data) + return + + +def load_data( + filename, minrows=10, headers=False, hdel="=", hignore=None, **kwargs ): """Find and load data from a text file. @@ -31,7 +221,7 @@ def loadData( Parameters ---------- - filename + filename: Path or string Name of the file we want to load data from. minrows: int Minimum number of rows in the first data block. All rows must have @@ -66,8 +256,8 @@ def loadData( comma-separated data blocks, set delimiter to ','. unpack: bool Return data as a sequence of columns that allows tuple unpacking such - as x, y = loadData(FILENAME, unpack=True). Note transposing the - loaded array as loadData(FILENAME).T has the same effect. + as x, y = load_data(FILENAME, unpack=True). Note transposing the + loaded array as load_data(FILENAME).T has the same effect. usecols: Zero-based index of columns to be loaded, by default use all detected columns. The reading skips data blocks that do not have the usecols- @@ -115,10 +305,11 @@ def countcolumnsvalues(line): return nc, nv # Check if file exists before trying to open - if not os.path.exists(filename): + filename = Path(filename) + if not filename.is_file(): raise IOError( ( - f"File {filename} cannot be found. " + f"File {str(filename)} cannot be found. " "Please rerun the program specifying a valid filename." ) ) @@ -196,169 +387,3 @@ def countcolumnsvalues(line): kwargs.setdefault("usecols", list(range(ncvblock[0]))) data_block = loadtxt(fid, **kwargs) return data_block - - -class TextDataLoader(object): - """Smart loading of a text data with possibly multiple datasets. - - Parameters - ---------- - minrows: int - Minimum number of rows in the first data block. (Default 10.) - usecols: tuple - Which columns in our dataset to use. Ignores all other columns. If - None (default), use all columns. - skiprows - Rows in dataset to skip. (Currently not functional.) - """ - - def __init__(self, minrows=10, usecols=None, skiprows=None): - if minrows is not None: - self.minrows = minrows - if usecols is not None: - self.usecols = tuple(usecols) - # FIXME: implement usage in _findDataBlocks - if skiprows is not None: - self.skiprows = skiprows - # data items - self._reset() - return - - def _reset(self): - self.filename = "" - self.headers = [] - self.datasets = [] - self._resetvars() - return - - def _resetvars(self): - self._filename = "" - self._lines = None - self._splitlines = None - self._words = None - self._linerecs = None - self._wordrecs = None - return - - def read(self, filename): - """Open a file and run readfp. - - Use if file is not already open for read byte. - """ - with open(filename, "rb") as fp: - self.readfp(fp) - return - - def readfp(self, fp, append=False): - """Get file details. - - File details include: - * File name. - * All data blocks findable by loadData. - * Headers (if present) for each data block. (Generally the headers - contain column name information). - """ - self._reset() - # try to read lines from fp first - self._lines = fp.readlines() - # and if good, assign filename - self.filename = getattr(fp, "name", "") - self._words = "".join(self._lines).split() - self._splitlines = [line.split() for line in self._lines] - self._findDataBlocks() - return - - def _findDataBlocks(self): - mincols = 1 - if self.usecols is not None and len(self.usecols): - mincols = max(mincols, max(self.usecols) + 1) - mincols = max(mincols, abs(min(self.usecols))) - nlines = len(self._lines) - nwords = len(self._words) - # idx - line index, nw0, nw1 - index of the first and last word, - # nf - number of words, ok - has data - self._linerecs = numpy.recarray( - (nlines,), - dtype=[ - ("idx", int), - ("nw0", int), - ("nw1", int), - ("nf", int), - ("ok", bool), - ], - ) - lr = self._linerecs - lr.idx = numpy.arange(nlines) - lr.nf = [len(sl) for sl in self._splitlines] - lr.nw1 = lr.nf.cumsum() - lr.nw0 = lr.nw1 - lr.nf - lr.ok = True - # word records - lw = self._wordrecs = numpy.recarray( - (nwords,), - dtype=[ - ("idx", int), - ("line", int), - ("col", int), - ("ok", bool), - ("value", float), - ], - ) - lw.idx = numpy.arange(nwords) - n1 = numpy.zeros(nwords, dtype=bool) - n1[lr.nw1[:-1]] = True - lw.line = n1.cumsum() - lw.col = lw.idx - lr.nw0[lw.line] - lw.ok = True - values = nwords * [0.0] - for i, w in enumerate(self._words): - try: - values[i] = float(w) - except ValueError: - lw.ok[i] = False - # prune lines that have a non-float values: - lw.values = values - if self.usecols is None: - badlines = lw.line[~lw.ok] - lr.ok[badlines] = False - else: - for col in self.usecols: - badlines = lw.line[(lw.col == col) & ~lw.ok] - lr.ok[badlines] = False - lr1 = lr[lr.nf >= mincols] - okb = numpy.r_[lr1.ok[:1], lr1.ok[1:] & ~lr1.ok[:-1], False] - oke = numpy.r_[False, ~lr1.ok[1:] & lr1.ok[:-1], lr1.ok[-1:]] - blockb = numpy.r_[True, lr1.nf[1:] != lr1.nf[:-1], False] - blocke = numpy.r_[False, blockb[1:-1], True] - beg = numpy.nonzero(okb | blockb)[0] - end = numpy.nonzero(oke | blocke)[0] - rowcounts = end - beg - assert not numpy.any(rowcounts < 0) - goodrows = rowcounts >= self.minrows - begend = numpy.transpose([beg, end - 1])[goodrows] - hbeg = 0 - for dbeg, dend in begend: - bb1 = lr1[dbeg] - ee1 = lr1[dend] - hend = bb1.idx - header = "".join(self._lines[hbeg:hend]) - hbeg = ee1.idx + 1 - if self.usecols is None: - data = numpy.reshape(lw.value[bb1.nw0 : ee1.nw1], (-1, bb1.nf)) - else: - tdata = numpy.empty( - (len(self.usecols), dend - dbeg), dtype=float - ) - for j, trow in zip(self.usecols, tdata): - j %= bb1.nf - trow[:] = lw.value[bb1.nw0 + j : ee1.nw1 : bb1.nf] - data = tdata.transpose() - self.headers.append(header) - self.datasets.append(data) - # finish reading to a last header and empty dataset - if hbeg < len(self._lines): - header = "".join(self._lines[hbeg:]) - data = numpy.empty(0, dtype=float) - self.headers.append(header) - self.datasets.append(data) - return diff --git a/src/diffpy/utils/parsers/serialization.py b/src/diffpy/utils/parsers/serialization.py index 7531c77f..46e29d2e 100644 --- a/src/diffpy/utils/parsers/serialization.py +++ b/src/diffpy/utils/parsers/serialization.py @@ -33,10 +33,12 @@ def serialize_data( show_path=True, serial_file=None, ): - """Serialize file data into a dictionary. Can also save dictionary into a - serial language file. Dictionary is formatted as {filename: data}. + """Serialize file data into a dictionary. - Requires hdata and data_table (can be generated by loadData). + Can also save dictionary into a serial language file. + Dictionary is formatted as {filename:data}. + + Requires hdata and data_table (can be generated by load_data). Parameters ---------- @@ -66,7 +68,6 @@ def serialize_data( dict: Returns the dictionary loaded from/into the updated database file. """ - # compile data_table and hddata together data = {} @@ -190,7 +191,6 @@ def deserialize_data(filename, filetype=None): dict A dictionary read from a serial file. """ - # check if supported type f = pathlib.Path(filename) f_name = f.name diff --git a/src/diffpy/utils/resampler.py b/src/diffpy/utils/resampler.py index ca93761c..1e0f035d 100644 --- a/src/diffpy/utils/resampler.py +++ b/src/diffpy/utils/resampler.py @@ -30,15 +30,15 @@ def wsinterp(x, xp, fp, left=None, right=None): Parameters ---------- - x: ndarray + x: ``ndarray`` The x values at which interpolation is computed. - xp: ndarray + xp: ``ndarray`` The array of known x values. - fp: ndarray + fp: ``ndarray`` The array of y values associated with xp. left: float If given, set fp for x < xp[0] to left. Otherwise, if left is None - (default) or not given, set fp for x < xp[0] to fp evaluated at xp[-1]. + (default) or not given, set fp for x < xp[0] to fp evaluated at xp[0]. right: float If given, set fp for x > xp[-1] to right. Otherwise, if right is None (default) or not given, set fp for x > xp[-1] to fp evaluated at @@ -46,7 +46,7 @@ def wsinterp(x, xp, fp, left=None, right=None): Returns ------- - ndarray or float + ``ndarray`` or float The interpolated values at points x. Returns a single float if x is a scalar, otherwise returns a numpy.ndarray. """ @@ -80,8 +80,8 @@ def wsinterp(x, xp, fp, left=None, right=None): def nsinterp(xp, fp, qmin=0, qmax=25, left=None, right=None): - """One-dimensional Whittaker-Shannon interpolation onto the Nyquist-Shannon - grid. + """One-dimensional Whittaker-Shannon interpolation onto the Nyquist- + Shannon grid. Takes a band-limited function fp and original grid xp and resamples fp on the NS grid. Uses the minimum number of points N required by the Nyquist @@ -91,9 +91,9 @@ def nsinterp(xp, fp, qmin=0, qmax=25, left=None, right=None): Parameters ---------- - xp: ndarray + xp: ``ndarray`` The array of known x values. - fp: ndarray + fp: ``ndarray`` The array of y values associated with xp. qmin: float The lower band limit in the frequency domain. @@ -102,7 +102,7 @@ def nsinterp(xp, fp, qmin=0, qmax=25, left=None, right=None): Returns ------- - x: ndarray + x: ``ndarray`` The Nyquist-Shannon grid computed for the given qmin and qmax. fp_at_x: ndarray The interpolated values at points x. Returns a single float if x is a @@ -139,9 +139,8 @@ def resample(r, s, dr): Returns ------- - Returns resampled (r, s). + Returns resampled ``(r, s)``. """ - warnings.warn( ( "The 'resample' function is deprecated and will be removed " diff --git a/src/diffpy/utils/tools.py b/src/diffpy/utils/tools.py index 63e10ba2..42e43bc8 100644 --- a/src/diffpy/utils/tools.py +++ b/src/diffpy/utils/tools.py @@ -8,7 +8,7 @@ from scipy.signal import convolve from xraydb import material_mu -from diffpy.utils.parsers.loaddata import loadData +from diffpy.utils.parsers import load_data def _stringify(string_value): @@ -51,43 +51,46 @@ def _load_config(file_path): def get_user_info(owner_name=None, owner_email=None, owner_orcid=None): - """Get name, email, and orcid of the owner/user from various sources and - return it as a metadata dictionary. - - The function looks for the information in json format configuration files - with the name 'diffpyconfig.json'. These can be in the user's home - directory and in the current working directory. The information in the - config files are combined, with the local config overriding the - home- directory one. Values for owner_name, owner_email, and owner_orcid - may be passed in to the function and these override the values in the - config files. - - A template for the config file is below. Create a text file called ' - diffpyconfig.json' in your home directory and copy-paste the template - into it, editing it with your real information. - { - "owner_name": ">", - "owner_email": ">@email.com", - "owner_orcid": ">" # noqa: E501 - } + """Get name, email, and ORCID of the owner/user from various sources + and return it as a metadata dictionary. + + The function looks for information in JSON configuration files named + ``diffpyconfig.json``. These can be in the user's home directory and in + the current working directory. The information in the config files is + combined, with the local config overriding the home-directory one. + Values for ``owner_name``, ``owner_email``, and ``owner_orcid`` may be + passed in to the function, and these override the config files. + + A template for the config file is below. Create a text file called + ``diffpyconfig.json`` in your home directory and paste the template into + it, editing it with your real information:: + + { + "owner_name": "", + "owner_email": "@email.com", + "owner_orcid": "" # noqa: E501 + } + You may also store any other global-level information that you would like - associated with your diffraction data in this file + associated with your diffraction data in this file. Parameters ---------- - owner_name : str, optional, default is the value stored in the global or - local config file. The name of the user who will show as owner in the - metadata that is stored with the data - owner_email : str, optional, default is the value stored in the global or - local config file. The email of the user/owner - owner_orcid : str, optional, default is the value stored in the global or - local config file. The ORCID id of the user/owner + owner_name : str, ``optional`` + Default is the value stored in the global or local config file. + The name of the user stored in metadata. + owner_email : str, ``optional`` + Default is the value stored in the global or local config file. + The email address of the user/owner. + owner_orcid : str, ``optional`` + Default is the value stored in the global or local config file. + The ORCID ID of the user/owner. Returns ------- user_info : dict - The dictionary containing username, email and orcid of the user/owner - , and any other information stored in the global or local config files. + Dictionary containing username, email, ORCID, and any other + information stored in global or local config files. """ runtime_info = { "owner_name": owner_name, @@ -106,8 +109,8 @@ def get_user_info(owner_name=None, owner_email=None, owner_orcid=None): def check_and_build_global_config(skip_config_creation=False): - """Check for a global diffpu config file in user's home directory and - creates one if it is missing. + """Check for a global diffpu config file in user's home directory + and creates one if it is missing. The file it looks for is called diffpyconfig.json. This can contain anything in json format, but minimally contains information about the @@ -127,9 +130,9 @@ def check_and_build_global_config(skip_config_creation=False): Parameters ---------- - skip_config_creation : bool, optional, default is False. + skip_config_creation : bool, ``optional`` The boolean that will override the creation workflow even if no - config file exists. + config file exists. Default is False. Returns ------- @@ -190,6 +193,7 @@ def get_package_info(package_names, metadata=None): Package info stored in metadata as {'package_info': {'package_name': 'version_number'}}. + Parameters ---------- package_name : str or list The name of the package(s) to retrieve the version number for. @@ -227,46 +231,30 @@ def get_density_from_cloud(sample_composition, mp_token=""): ) -def compute_mu_using_xraydb( - sample_composition, energy, sample_mass_density=None, packing_fraction=None -): - """Compute the attenuation coefficient (mu) using the XrayDB database. +def compute_mu_using_xraydb(sample_composition, energy, sample_mass_density): + """Compute the attenuation coefficient (mu) using the XrayDB + database. - Computes mu based on the sample composition and energy. - User should provide a sample mass density or a packing fraction. - If neither density nor packing fraction is specified, - or if both are specified, a ValueError will be raised. - Reference: https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu. + Computes mu based on the sample composition, X-ray energy, and + sample mass density. + + Reference: + https://xraypy.github.io/XrayDB/python.html#xraydb.material_mu Parameters ---------- sample_composition : str The chemical formula of the material. energy : float - The energy of the incident x-rays in keV. - sample_mass_density : float, optional, Default is None - The mass density of the packed powder/sample in g/cm*3. - packing_fraction : float, optional, Default is None - The fraction of sample in the capillary (between 0 and 1). - Specify either sample_mass_density or packing_fraction but not both. + The energy of the incident X-rays in keV. + sample_mass_density : float + The mass density of the sample in g/cm^3. Returns ------- mu : float - The attenuation coefficient mu in mm^{-1}. + The attenuation coefficient μ in mm⁻¹. """ - if (sample_mass_density is None and packing_fraction is None) or ( - sample_mass_density is not None and packing_fraction is not None - ): - raise ValueError( - "You must specify either sample_mass_density or packing_fraction, " - "but not both. " - "Please rerun specifying only one." - ) - if packing_fraction is not None: - sample_mass_density = ( - get_density_from_cloud(sample_composition) * packing_fraction - ) energy_eV = energy * 1000 mu = ( material_mu( @@ -281,8 +269,8 @@ def compute_mu_using_xraydb( def _top_hat(z, half_slit_width): - """Create a top-hat function, return 1.0 for values within the specified - slit width and 0 otherwise.""" + """Create a top-hat function, return 1.0 for values within the + specified slit width and 0 otherwise.""" return np.where((z >= -half_slit_width) & (z <= half_slit_width), 1.0, 0.0) @@ -313,9 +301,10 @@ def _model_function(z, diameter, z0, I0, mud, slope): def _extend_z_and_convolve(z, diameter, half_slit_width, z0, I0, mud, slope): - """Extend z values and I values for padding (so that we don't have tails in - convolution), then perform convolution (note that the convolved I values - are the same as modeled I values if slit width is close to 0)""" + """Extend z values and I values for padding (so that we don't have + tails in convolution), then perform convolution (note that the + convolved I values are the same as modeled I values if slit width is + close to 0)""" n_points = len(z) z_left_pad = np.linspace( z.min() - n_points * (z[1] - z[0]), z.min(), n_points @@ -336,8 +325,8 @@ def _extend_z_and_convolve(z, diameter, half_slit_width, z0, I0, mud, slope): def _objective_function(params, z, observed_data): """Compute the objective function for fitting a model to the - observed/experimental data by minimizing the sum of squared residuals - between the observed data and the convolved model data.""" + observed/experimental data by minimizing the sum of squared + residuals between the observed data and the convolved model data.""" diameter, half_slit_width, z0, I0, mud, slope = params convolved_model_data = _extend_z_and_convolve( z, diameter, half_slit_width, z0, I0, mud, slope @@ -347,7 +336,8 @@ def _objective_function(params, z, observed_data): def _compute_single_mud(z_data, I_data): - """Perform dual annealing optimization and extract the parameters.""" + """Perform dual annealing optimization and extract the + parameters.""" bounds = [ ( 1e-5, @@ -376,8 +366,8 @@ def _compute_single_mud(z_data, I_data): def compute_mud(filepath): - """Compute the best-fit mu*D value from a z-scan file, removing the sample - holder effect. + """Compute the best-fit mu*D value from a z-scan file, removing the + sample holder effect. This function loads z-scan data and fits it to a model that convolves a top-hat function with I = I0 * e^{-mu * l}. @@ -400,7 +390,7 @@ def compute_mud(filepath): mu*D : float The best-fit mu*D value. """ - z_data, I_data = loadData(filepath, unpack=True) + z_data, I_data = load_data(filepath, unpack=True) best_mud, _ = min( (_compute_single_mud(z_data, I_data) for _ in range(20)), key=lambda pair: pair[1], diff --git a/src/diffpy/utils/transforms.py b/src/diffpy/utils/transforms.py index 56eebc68..8cb07605 100644 --- a/src/diffpy/utils/transforms.py +++ b/src/diffpy/utils/transforms.py @@ -52,7 +52,7 @@ def q_to_tth(q, wavelength): Parameters ---------- - q : ndarray + q : ``ndarray`` The 1D array of :math:`q` values numpy.array([qs]). The units of q must be reciprocal of the units of wavelength. @@ -61,7 +61,7 @@ def q_to_tth(q, wavelength): Returns ------- - tth : ndarray + tth : ``ndarray`` The 1D array of :math:`2\theta` values in degrees numpy.array([tths]). """ _validate_inputs(q, wavelength) @@ -76,7 +76,8 @@ def q_to_tth(q, wavelength): def tth_to_q(tth, wavelength): - r"""Helper function to convert two-theta to q on independent variable axis. + r"""Helper function to convert two-theta to q on independent variable + axis. If wavelength is missing, returns independent variable axis as integer indexes. @@ -95,7 +96,7 @@ def tth_to_q(tth, wavelength): Parameters ---------- - tth : ndarray + tth : ``ndarray`` The 1D array of :math:`2\theta` values np.array([tths]). The units of tth are expected in degrees. @@ -104,7 +105,7 @@ def tth_to_q(tth, wavelength): Returns ------- - q : ndarray + q : ``ndarray`` The 1D array of :math:`q` values np.array([qs]). The units for the q-values are the inverse of the units of the provided wavelength. @@ -124,18 +125,18 @@ def tth_to_q(tth, wavelength): def q_to_d(q): - r"""Helper function to convert q to d on independent variable axis, using - :math:`d = \frac{2 \pi}{q}`. + r"""Helper function to convert q to d on independent variable axis, + using :math:`d = \frac{2 \pi}{q}`. Parameters ---------- - q : ndarray + q : ``ndarray`` The 1D array of :math:`q` values np.array([qs]). The units of q must be reciprocal of the units of wavelength. Returns ------- - d : ndarray + d : ``ndarray`` The 1D array of :math:`d` values np.array([ds]). """ if 0 in q: @@ -144,7 +145,8 @@ def q_to_d(q): def tth_to_d(tth, wavelength): - r"""Helper function to convert two-theta to d on independent variable axis. + r"""Helper function to convert two-theta to d on independent variable + axis. The formula is .. math:: d = \frac{\lambda}{2 \sin\left(\frac{2\theta}{2}\right)}. @@ -153,7 +155,7 @@ def tth_to_d(tth, wavelength): Parameters ---------- - tth : nsarray + tth : ``nsarray`` The 1D array of :math:`2\theta` values np.array([tths]). The units of tth are expected in degrees. @@ -162,7 +164,7 @@ def tth_to_d(tth, wavelength): Returns ------- - d : nsarray + d : ``nsarray`` The 1D array of :math:`d` values np.array([ds]). """ q = tth_to_q(tth, wavelength) @@ -178,16 +180,17 @@ def tth_to_d(tth, wavelength): def d_to_q(d): - r"""Helper function to convert q to d using :math:`d = \frac{2 \pi}{q}`. + r"""Helper function to convert q to d using :math:`d = \frac{2 + \pi}{q}`. Parameters ---------- - d : nsarray + d : ``nsarray`` The 1D array of :math:`d` values np.array([ds]). Returns ------- - q : nsarray + q : ``nsarray`` The 1D array of :math:`q` values np.array([qs]). The units of q must be reciprocal of the units of wavelength. """ @@ -197,7 +200,8 @@ def d_to_q(d): def d_to_tth(d, wavelength): - r"""Helper function to convert d to two-theta on independent variable axis. + r"""Helper function to convert d to two-theta on independent variable + axis. The formula is .. math:: 2\theta = 2 \arcsin\left(\frac{\lambda}{2d}\right). @@ -206,7 +210,7 @@ def d_to_tth(d, wavelength): Parameters ---------- - d : nsarray + d : ``nsarray`` The 1D array of :math:`d` values np.array([ds]). wavelength : float @@ -214,7 +218,7 @@ def d_to_tth(d, wavelength): Returns ------- - tth : nsarray + tth : ``nsarray`` The 1D array of :math:`2\theta` values np.array([tths]). The units of tth are expected in degrees. """ diff --git a/src/diffpy/utils/utils_app.py b/src/diffpy/utils/utils_app.py new file mode 100644 index 00000000..588e28c9 --- /dev/null +++ b/src/diffpy/utils/utils_app.py @@ -0,0 +1,33 @@ +import argparse + +from diffpy.utils.version import __version__ # noqa + + +def main(): + parser = argparse.ArgumentParser( + prog="diffpy.utils", + description=( + "Shared utilities for diffpy packages.\n\n" + "For more information, visit: " + "https://github.com/diffpy/diffpy.utils/" + ), + formatter_class=argparse.RawDescriptionHelpFormatter, + ) + + parser.add_argument( + "--version", + action="store_true", + help="Show the program's version number and exit", + ) + + args = parser.parse_args() + + if args.version: + print(f"diffpy.utils {__version__}") + else: + # Default behavior when no arguments are given + parser.print_help() + + +if __name__ == "__main__": + main() diff --git a/src/diffpy/utils/version.py b/src/diffpy/utils/version.py index a17ccb5c..d94610ae 100644 --- a/src/diffpy/utils/version.py +++ b/src/diffpy/utils/version.py @@ -18,8 +18,9 @@ # __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"] # obtain version information -from importlib.metadata import version +from importlib.metadata import PackageNotFoundError, version -__version__ = version("diffpy.utils") - -# End of file +try: + __version__ = version("diffpy.utils") +except PackageNotFoundError: + __version__ = "unknown" diff --git a/src/diffpy/utils/wx/gridutils.py b/src/diffpy/utils/wx/gridutils.py index d6f2874a..f585cc41 100644 --- a/src/diffpy/utils/wx/gridutils.py +++ b/src/diffpy/utils/wx/gridutils.py @@ -81,8 +81,9 @@ def getSelectedCells(grid): def limitSelectionToRows(grid, indices): - """Limit selection to the specified row indices. No action for empty - indices. + """Limit selection to the specified row indices. + + No action for empty indices. Parameters ---------- @@ -146,9 +147,9 @@ def quickResizeColumns(grid, indices): def _indicesToBlocks(indices): - """Convert a list of integer indices to a list of (start, stop) tuples. The - (start, stop) tuple defines a continuous block, where the stop index is - included in the block. + """Convert a list of integer indices to a list of (start, stop) + tuples. The (start, stop) tuple defines a continuous block, where + the stop index is included in the block. Parameters ---------- diff --git a/tests/test_deprecator.py b/tests/test_deprecator.py new file mode 100644 index 00000000..c4f2d25b --- /dev/null +++ b/tests/test_deprecator.py @@ -0,0 +1,38 @@ +import pytest + +from diffpy.utils._deprecator import build_deprecation_message, deprecated + +old_base = "diffpy.utils" +old_name = "oldFunction" +new_name = "new_function" +removal_version = "4.0.0" + +dep_msg = build_deprecation_message( + old_base, old_name, new_name, removal_version +) + + +@deprecated(dep_msg) +def oldFunction(print_msg): + """This function is deprecated and will be removed in version 4.0.0. + + Please use newFunction instead + """ + return new_function(print_msg) + + +def new_function(print_msg): + print(print_msg) + return + + +def test_deprecated(capsys): + # Case: user deprecates a function with the deprecated decorator + # Expected: DeprecationWarning is raised when the function is called + # and the function executes correctly + expected_print_msg = "Testing deprecated function" + with pytest.deprecated_call(match=dep_msg): + oldFunction(expected_print_msg) + captured = capsys.readouterr() + actual_print_msg = captured.out.strip() + assert actual_print_msg == expected_print_msg diff --git a/tests/test_diffraction_objects.py b/tests/test_diffraction_objects.py index 8ed1dd3b..59ee5934 100644 --- a/tests/test_diffraction_objects.py +++ b/tests/test_diffraction_objects.py @@ -376,8 +376,8 @@ def test_scale_to_bad(org_do_args, target_do_args, scale_inputs): }, 0, ), - ( # C2: Target value lies in the array, expect the (first) closest - # index + # C2: Target value lies in the array, expect the closest index + ( # 1. xtype(tth) is equal to self._input_xtype(tth) { "wavelength": 4 * np.pi, "xarray": np.array([30, 60]), @@ -390,7 +390,7 @@ def test_scale_to_bad(org_do_args, target_do_args, scale_inputs): }, 0, ), - ( + ( # 2. use default xtype(equal to self._input_xtype) { "wavelength": 4 * np.pi, "xarray": np.array([30, 60]), @@ -398,11 +398,24 @@ def test_scale_to_bad(org_do_args, target_do_args, scale_inputs): "xtype": "tth", }, { - "xtype": "q", - "value": 0.25, + "xtype": None, + "value": 45, }, 0, ), + ( # 3. xtype(q) is different from self._input_xtype(tth) + { + "wavelength": 4 * np.pi, + "xarray": np.array([30, 60]), + "yarray": np.array([1, 2]), + "xtype": "tth", + }, + { + "xtype": "q", + "value": 0.5, + }, + 1, + ), # C3: Target value out of the range, expect the closest index ( # 1. Test with xtype of "q" { @@ -435,12 +448,13 @@ def test_scale_to_bad(org_do_args, target_do_args, scale_inputs): def test_get_array_index(do_args, get_array_index_inputs, expected_index): do = DiffractionObject(**do_args) actual_index = do.get_array_index( - get_array_index_inputs["xtype"], get_array_index_inputs["value"] + get_array_index_inputs["value"], get_array_index_inputs["xtype"] ) assert actual_index == expected_index def test_get_array_index_bad(): + # empty array in DiffractionObject do = DiffractionObject( wavelength=2 * np.pi, xarray=np.array([]), @@ -454,6 +468,22 @@ def test_get_array_index_bad(): ), ): do.get_array_index(xtype="tth", xvalue=30) + # non-existing xtype + do = DiffractionObject( + wavelength=4 * np.pi, + xarray=np.array([30, 60]), + yarray=np.array([1, 2]), + xtype="tth", + ) + non_existing_xtype = "non_existing_xtype" + with pytest.raises( + ValueError, + match=re.escape( + f"I don't know how to handle the xtype, '{non_existing_xtype}'. " + f"Please rerun specifying an xtype from {*XQUANTITIES, }" + ), + ): + do.get_array_index(xtype=non_existing_xtype, xvalue=30) def test_dump(tmp_path, mocker): diff --git a/tests/test_loaddata.py b/tests/test_loaddata.py index 82d947ee..92c53571 100644 --- a/tests/test_loaddata.py +++ b/tests/test_loaddata.py @@ -5,6 +5,7 @@ import numpy as np import pytest +from diffpy.utils.parsers import load_data from diffpy.utils.parsers.loaddata import loadData @@ -80,3 +81,77 @@ def test_loadData_headers(datafile): loaddatawithheaders, headers=True, hdel=delimiter, hignore=hignore ) assert hdata == expected + + +def test_load_data_default(datafile): + """Check load_data() with default options.""" + loaddata01 = datafile("loaddata01.txt") + d2c = np.array([[3, 31], [4, 32], [5, 33]]) + + with pytest.raises(IOError) as err: + load_data("doesnotexist.txt") + assert str(err.value) == ( + "File doesnotexist.txt cannot be found. " + "Please rerun the program specifying a valid filename." + ) + + # The default minrows=10 makes it read from the third line + d = load_data(loaddata01) + assert np.array_equal(d2c, d) + + # The usecols=(0, 1) would make it read from the third line + d = load_data(loaddata01, minrows=1, usecols=(0, 1)) + assert np.array_equal(d2c, d) + + # Check the effect of usecols effect + d = load_data(loaddata01, usecols=(0,)) + assert np.array_equal(d2c[:, 0], d) + + d = load_data(loaddata01, usecols=(1,)) + assert np.array_equal(d2c[:, 1], d) + + +def test_load_data_1column(datafile): + """Check loading of one-column data.""" + loaddata01 = datafile("loaddata01.txt") + d1c = np.arange(1, 6) + + # Assertions using pytest's assert + d = load_data(loaddata01, usecols=[0], minrows=1) + assert np.array_equal(d1c, d) + + d = load_data(loaddata01, usecols=[0], minrows=2) + assert np.array_equal(d1c, d) + + d = load_data(loaddata01, usecols=[0], minrows=3) + assert not np.array_equal(d1c, d) + + +def test_load_data_headers(datafile): + """Check loadData() with headers options enabled.""" + expected = { + "wavelength": 0.1, + "dataformat": "Qnm", + "inputfile": "darkSub_rh20_C_01.chi", + "mode": "xray", + "bgscale": 1.2998929285, + "composition": "0.800.20", + "outputtype": "gr", + "qmaxinst": 25.0, + "qmin": 0.1, + "qmax": 25.0, + "rmax": "100.0r", + "rmin": "0.0r", + "rstep": "0.01r", + "rpoly": "0.9r", + } + + loaddatawithheaders = datafile("loaddatawithheaders.txt") + hignore = ["# ", "// ", "["] # ignore lines beginning with these strings + delimiter = ": " # what our data should be separated by + + # Load data with headers + hdata = load_data( + loaddatawithheaders, headers=True, hdel=delimiter, hignore=hignore + ) + assert hdata == expected diff --git a/tests/test_serialization.py b/tests/test_serialization.py index 039877f6..eeab5307 100644 --- a/tests/test_serialization.py +++ b/tests/test_serialization.py @@ -3,11 +3,11 @@ import numpy import pytest +from diffpy.utils.parsers import load_data from diffpy.utils.parsers.custom_exceptions import ( ImproperSizeError, UnsupportedTypeError, ) -from diffpy.utils.parsers.loaddata import loadData from diffpy.utils.parsers.serialization import deserialize_data, serialize_data @@ -21,9 +21,9 @@ def test_load_multiple(tmp_path, datafile): generated_data = None for headerfile in tlm_list: - # gather data using loadData - hdata = loadData(headerfile, headers=True) - data_table = loadData(headerfile) + # gather data using load_data + hdata = load_data(headerfile, headers=True) + data_table = load_data(headerfile) # check path extraction generated_data = serialize_data( @@ -33,7 +33,9 @@ def test_load_multiple(tmp_path, datafile): dt_colnames=["r", "gr"], show_path=True, ) - assert headerfile == Path(generated_data[headerfile.name].pop("path")) + assert Path(headerfile).resolve() == Path( + generated_data[headerfile.name].pop("path") + ) # rerun without path information and save to file generated_data = serialize_data( @@ -58,8 +60,8 @@ def test_exceptions(datafile): loadfile = datafile("loadfile.txt") warningfile = datafile("generatewarnings.txt") nodt = datafile("loaddatawithheaders.txt") - hdata = loadData(loadfile, headers=True) - data_table = loadData(loadfile) + hdata = load_data(loadfile, headers=True) + data_table = load_data(loadfile) # improper file types with pytest.raises(UnsupportedTypeError): @@ -121,15 +123,15 @@ def test_exceptions(datafile): assert numpy.allclose(r_extract[data_name]["r"], r_list) assert numpy.allclose(gr_extract[data_name]["gr"], gr_list) # no datatable - nodt_hdata = loadData(nodt, headers=True) - nodt_dt = loadData(nodt) + nodt_hdata = load_data(nodt, headers=True) + nodt_dt = load_data(nodt) no_dt = serialize_data(nodt, nodt_hdata, nodt_dt, show_path=False) nodt_data_name = list(no_dt.keys())[0] assert numpy.allclose(no_dt[nodt_data_name]["data table"], nodt_dt) # ensure user is warned when columns are overwritten - hdata = loadData(warningfile, headers=True) - data_table = loadData(warningfile) + hdata = load_data(warningfile, headers=True) + data_table = load_data(warningfile) with pytest.warns(RuntimeWarning) as record: serialize_data( warningfile, diff --git a/tests/test_tools.py b/tests/test_tools.py index 6be3870f..18c30fe3 100644 --- a/tests/test_tools.py +++ b/tests/test_tools.py @@ -9,7 +9,6 @@ from diffpy.utils.tools import ( _extend_z_and_convolve, check_and_build_global_config, - compute_mu_using_xraydb, compute_mud, get_package_info, get_user_info, @@ -270,40 +269,6 @@ def test_get_package_info(monkeypatch, inputs, expected): assert actual_metadata == expected -@pytest.mark.parametrize( - "inputs", - [ - # Test when the function has invalid inputs - ( # C1: Both mass density and packing fraction are provided, - # expect ValueError exception - { - "sample_composition": "SiO2", - "energy": 10, - "sample_mass_density": 2.65, - "packing_fraction": 1, - } - ), - ( # C2: None of mass density or packing fraction are provided, - # expect ValueError exception - { - "sample_composition": "SiO2", - "energy": 10, - } - ), - ], -) -def test_compute_mu_using_xraydb_bad(inputs): - with pytest.raises( - ValueError, - match=( - "You must specify either sample_mass_density or " - "packing_fraction, but not both. " - "Please rerun specifying only one." - ), - ): - compute_mu_using_xraydb(**inputs) - - def test_compute_mud(tmp_path): diameter, slit_width, z0, I0, mud, slope = 1, 0.1, 0, 1e5, 3, 0 z_data = np.linspace(-1, 1, 50)