Fix missing files in packaging

.github/workflows/CI_CD_actions.yml

@@ -30,13 +30,14 @@ jobs:
           python-version: 3.7
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
+          python -m pip install -U pip
           pip install .
-          pip install -U -r requirements_dev.txt
+          python -m pip install -U -r requirements_dev.txt
       - name: Show installed packages
         run: pip freeze
       - name: Build docs
         run: |
+          python docs/source/generate_api_doc.py
           make --directory=docs clean html
 
   docs-links:
@@ -50,15 +51,41 @@ jobs:
           python-version: 3.7
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
+          python -m pip install -U pip
           pip install .
-          pip install -U -r requirements_dev.txt
+          python -m pip install -U -r requirements_dev.txt
       - name: Show installed packages
         run: pip freeze
       - name: Check doc links
         run: |
+          python docs/source/generate_api_doc.py
           make --directory=docs clean linkcheck
 
+  api-docs-up-to-date:
+    runs-on: [ubuntu-latest]
+    needs: [test]
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          pip install .
+      - name: Show installed packages
+        run: pip freeze
+      - name: Check if api docs are outdated
+        run: |
+          mv docs/source/user_documentation/api_documentation.rst current_api_docs.rst
+          python docs/source/generate_api_doc.py
+          diff -qywBd current_api_docs.rst docs/source/user_documentation/api_documentation.rst
+      - name: Fix instructions
+        if: failure()
+        run: echo run 'python docs/source/generate_api_doc.py' locally to fix this issue
+
+
   test:
     runs-on: ${{ matrix.os }}
     needs: [lint]
@@ -76,7 +103,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements_dev.txt
+          pip install .
+          python -m pip install -r requirements_dev.txt
       - name: Show installed packages
         run: pip freeze
       - name: Run tests
@@ -95,8 +123,8 @@ jobs:
           python-version: 3.7
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements_dev.txt
+          python -m pip install -U pip
+          python -m pip install -r requirements_dev.txt
       - name: Build dist
         run: |
           python setup.py sdist bdist_wheel

MANIFEST.in

@@ -0,0 +1,11 @@
+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.md
+include LICENSE
+include README.md
+setup.cfg
+setup.py
+
+recursive-include glotaran *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

docs/source/_templates/known_packages.rst

@@ -6,7 +6,7 @@
     afterwards.
 
 {% set known_packages=['glotaran.analysis', 'glotaran.builtin', 'glotaran.builtin.file_formats', 'glotaran.builtin.file_formats.ascii', 'glotaran.builtin.file_formats.sdt', 'glotaran.builtin.models', 'glotaran.builtin.models.doas', 'glotaran.builtin.models.kinetic_image', 'glotaran.builtin.models.kinetic_spectrum', 'glotaran.cli', 'glotaran.cli.commands', 'glotaran.examples', 'glotaran.io', 'glotaran.model', 'glotaran.parameter', 'glotaran.parse'] %}
-{% set child_modules=['glotaran.analysis', 'glotaran.analysis.matrix_calculation', 'glotaran.analysis.nnls', 'glotaran.analysis.optimize', 'glotaran.analysis.problem_bag', 'glotaran.analysis.residual_calculation', 'glotaran.analysis.result', 'glotaran.analysis.scheme', 'glotaran.analysis.simulation', 'glotaran.analysis.variable_projection', 'glotaran.builtin', 'glotaran.builtin.file_formats', 'glotaran.builtin.file_formats.ascii', 'glotaran.builtin.file_formats.ascii.wavelength_time_explicit_file', 'glotaran.builtin.file_formats.sdt', 'glotaran.builtin.file_formats.sdt.sdt_file', 'glotaran.builtin.file_formats.sdt.sdt_file_reader', 'glotaran.builtin.models', 'glotaran.builtin.models.doas', 'glotaran.builtin.models.doas.doas_matrix', 'glotaran.builtin.models.doas.doas_megacomplex', 'glotaran.builtin.models.doas.doas_model', 'glotaran.builtin.models.doas.doas_result', 'glotaran.builtin.models.doas.doas_spectral_matrix', 'glotaran.builtin.models.doas.oscillation', 'glotaran.builtin.models.kinetic_image', 'glotaran.builtin.models.kinetic_image.initial_concentration', 'glotaran.builtin.models.kinetic_image.irf', 'glotaran.builtin.models.kinetic_image.k_matrix', 'glotaran.builtin.models.kinetic_image.kinetic_image_dataset_descriptor', 'glotaran.builtin.models.kinetic_image.kinetic_image_matrix', 'glotaran.builtin.models.kinetic_image.kinetic_image_megacomplex', 'glotaran.builtin.models.kinetic_image.kinetic_image_model', 'glotaran.builtin.models.kinetic_image.kinetic_image_result', 'glotaran.builtin.models.kinetic_spectrum', 'glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_dataset_descriptor', 'glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_model', 'glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_result', 'glotaran.builtin.models.kinetic_spectrum.spectral_constraints', 'glotaran.builtin.models.kinetic_spectrum.spectral_irf', 'glotaran.builtin.models.kinetic_spectrum.spectral_matrix', 'glotaran.builtin.models.kinetic_spectrum.spectral_penalties', 'glotaran.builtin.models.kinetic_spectrum.spectral_relations', 'glotaran.builtin.models.kinetic_spectrum.spectral_shape', 'glotaran.cli', 'glotaran.cli.commands', 'glotaran.cli.commands.explore', 'glotaran.cli.commands.export', 'glotaran.cli.commands.optimize', 'glotaran.cli.commands.pluginlist', 'glotaran.cli.commands.print', 'glotaran.cli.commands.util', 'glotaran.cli.commands.validate', 'glotaran.cli.main', 'glotaran.examples', 'glotaran.examples.sequential', 'glotaran.io', 'glotaran.io.prepare_dataset', 'glotaran.io.reader', 'glotaran.model', 'glotaran.model.dataset_descriptor', 'glotaran.model.model', 'glotaran.model.model_attribute', 'glotaran.model.model_decorator', 'glotaran.model.model_property', 'glotaran.model.util', 'glotaran.parameter', 'glotaran.parameter.parameter', 'glotaran.parameter.parameter_group', 'glotaran.parse', 'glotaran.parse.parser', 'glotaran.parse.register'] %}
+{% set child_modules=['glotaran.analysis', 'glotaran.analysis.matrix_calculation', 'glotaran.analysis.nnls', 'glotaran.analysis.optimize', 'glotaran.analysis.problem_bag', 'glotaran.analysis.residual_calculation', 'glotaran.analysis.result', 'glotaran.analysis.scheme', 'glotaran.analysis.simulation', 'glotaran.analysis.variable_projection', 'glotaran.builtin', 'glotaran.builtin.file_formats', 'glotaran.builtin.file_formats.ascii', 'glotaran.builtin.file_formats.ascii.wavelength_time_explicit_file', 'glotaran.builtin.file_formats.sdt', 'glotaran.builtin.file_formats.sdt.sdt_file', 'glotaran.builtin.file_formats.sdt.sdt_file_reader', 'glotaran.builtin.models', 'glotaran.builtin.models.doas', 'glotaran.builtin.models.doas.doas_matrix', 'glotaran.builtin.models.doas.doas_megacomplex', 'glotaran.builtin.models.doas.doas_model', 'glotaran.builtin.models.doas.doas_result', 'glotaran.builtin.models.doas.doas_spectral_matrix', 'glotaran.builtin.models.doas.oscillation', 'glotaran.builtin.models.kinetic_image', 'glotaran.builtin.models.kinetic_image.initial_concentration', 'glotaran.builtin.models.kinetic_image.irf', 'glotaran.builtin.models.kinetic_image.k_matrix', 'glotaran.builtin.models.kinetic_image.kinetic_image_dataset_descriptor', 'glotaran.builtin.models.kinetic_image.kinetic_image_matrix', 'glotaran.builtin.models.kinetic_image.kinetic_image_megacomplex', 'glotaran.builtin.models.kinetic_image.kinetic_image_model', 'glotaran.builtin.models.kinetic_image.kinetic_image_result', 'glotaran.builtin.models.kinetic_spectrum', 'glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_dataset_descriptor', 'glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_matrix', 'glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_model', 'glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_result', 'glotaran.builtin.models.kinetic_spectrum.spectral_constraints', 'glotaran.builtin.models.kinetic_spectrum.spectral_irf', 'glotaran.builtin.models.kinetic_spectrum.spectral_matrix', 'glotaran.builtin.models.kinetic_spectrum.spectral_penalties', 'glotaran.builtin.models.kinetic_spectrum.spectral_relations', 'glotaran.builtin.models.kinetic_spectrum.spectral_shape', 'glotaran.cli', 'glotaran.cli.commands', 'glotaran.cli.commands.explore', 'glotaran.cli.commands.export', 'glotaran.cli.commands.optimize', 'glotaran.cli.commands.pluginlist', 'glotaran.cli.commands.print', 'glotaran.cli.commands.util', 'glotaran.cli.commands.validate', 'glotaran.cli.main', 'glotaran.examples', 'glotaran.examples.sequential', 'glotaran.io', 'glotaran.io.prepare_dataset', 'glotaran.io.reader', 'glotaran.model', 'glotaran.model.dataset_descriptor', 'glotaran.model.model', 'glotaran.model.model_attribute', 'glotaran.model.model_decorator', 'glotaran.model.model_property', 'glotaran.model.util', 'glotaran.parameter', 'glotaran.parameter.parameter', 'glotaran.parameter.parameter_group', 'glotaran.parse', 'glotaran.parse.parser', 'glotaran.parse.register'] %}
 {% block module %}
 
 {% endblock %}

docs/source/conf.py

@@ -123,7 +123,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.

docs/source/user_documentation/api_documentation.rst

@@ -51,6 +51,7 @@ The API Documentation for glotaran is automatically created from its docstrings.
     glotaran.builtin.models.kinetic_image.kinetic_image_result
     glotaran.builtin.models.kinetic_spectrum
     glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_dataset_descriptor
+    glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_matrix
     glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_model
     glotaran.builtin.models.kinetic_spectrum.kinetic_spectrum_result
     glotaran.builtin.models.kinetic_spectrum.spectral_constraints

setup.py

@@ -19,9 +19,9 @@
 # TODO: set a new genereal min version for netCDF4
 # when they deploy windows wheels again
 if sys.platform == "win32":
-    install_requires.append('netCDF4>=1.5,<1.5.3')
+    install_requires.append('netCDF4>=1.4,<=1.5.3')
 else:
-    install_requires.append('netCDF4>=1.5')
+    install_requires.append('netCDF4>=1.4')
 
 
 with open("README.md", "r") as fh:
@@ -56,7 +56,6 @@
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
-        'Programming Language :: Cython',
         'Topic :: Scientific/Engineering',
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
@@ -72,7 +71,7 @@
         'Source': 'https://github.com/glotaran/pyglotaran',
         'Tracker': 'https://github.com/glotaran/pyglotaran/issues',
     },
-    python_requires=">=3.6",
+    python_requires=">=3.6, <3.8",
     packages=find_packages(),
     install_requires=install_requires,
     entry_points=entry_points,

tox.ini

@@ -9,13 +9,15 @@ install_command = {envpython} -m pip install {opts} {packages}
 deps = -r{toxinidir}/requirements_dev.txt
 whitelist_externals = make
 commands =
+    {envpython} docs/source/generate_api_doc.py
     make --directory=docs clean html
 
 [testenv:docs-links]
 install_command = {envpython} -m pip install {opts} {packages}
 deps = -r{toxinidir}/requirements_dev.txt
 whitelist_externals = make
 commands =
+    {envpython} docs/source/generate_api_doc.py
     make --directory=docs clean linkcheck
 
 [testenv:flake8]