build!: define dev deps through requirements.txt

.github/workflows/cd.yml

@@ -1,4 +1,4 @@
-# cspell:ignore bdist noreply prereleased pypa sdist
+# cspell:ignore bdist noreply prereleased pypa reqs sdist
 
 name: CD
 
@@ -10,7 +10,7 @@ on:
 
 jobs:
   test:
-    name: Run pytest
+    name: Run pytest with unpinned dependencies
     if: startsWith(github.ref, 'refs/tags')
     runs-on: ${{ matrix.os }}
     strategy:
@@ -19,11 +19,6 @@ jobs:
           - macos-10.15
           - ubuntu-18.04
         python-version: [3.6, 3.7, 3.8]
-        exclude:
-          - os: macos-10.15
-            python-version: 3.6
-          - os: macos-10.15
-            python-version: 3.8
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -33,7 +28,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[test]
+          pip install -r .reqs/test.in
+          pip install .
       - name: Test with pytest
         env:
           PYTEST_RUN_SLOW_TESTS: YES
@@ -52,7 +48,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[doc]
+          pip install -r .reqs/doc.txt
+          pip install .
           sudo apt-get -y install pandoc graphviz
       - name: Build documentation and run notebooks
         working-directory: docs
@@ -76,7 +73,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[precommit]
+          pip install -r .reqs/sty.txt
+          pip install .
           sudo npm install -g cspell pyright
       - name: Perform style checks
         run: pre-commit run -a

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-# cspell:ignore unittests
+# cspell:ignore reqs unittests
 
 name: CI
 
@@ -31,7 +31,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[test]
+          pip install -r .reqs/test.txt
+          pip install .
       - name: Test with pytest-cov
         run: pytest -n auto --cov=tensorwaves --cov-report=xml
       - uses: codecov/codecov-action@v1
@@ -65,9 +66,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[test]
+          pip install -r .reqs/test.txt
+          pip install .
       - name: Test with pytest
-        run: pytest -n auto
+        run: pytest
       - name: Test example scripts
         working-directory: examples
         run: python *.py # https://github.com/ComPWA/tensorwaves/issues/103
@@ -85,7 +87,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[doc]
+          pip install -r .reqs/doc.txt
+          pip install .
           pip install tensorflow-cpu
           sudo apt-get -y install pandoc graphviz
       - name: Build documentation and run notebooks
@@ -110,7 +113,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[precommit]
+          pip install -r .reqs/sty.txt
+          pip install .
           sudo npm install -g cspell pyright
       - name: Perform style checks
         run: pre-commit run -a

.github/workflows/linkcheck.yml

@@ -1,3 +1,5 @@
+# cspell:ignore reqs
+
 name: Linkcheck
 
 on:
@@ -25,7 +27,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[doc]
+          pip install -r .reqs/doc.txt
           sudo apt-get -y install pandoc
       - name: Check external links
         working-directory: docs

.gitignore

@@ -51,4 +51,5 @@ pyvenv*/
 !environment.yml
 !pyrightconfig.json
 
+!docs/_static/*
 !examples/intensity-recipe.yaml

.gitpod.yml

@@ -1,5 +1,5 @@
 tasks:
-  - init: pip install -e .[dev]
+  - init: pip install -r requirements-dev.txt -e .
 
 github:
   prebuilds:

.pre-commit-config.yaml

@@ -19,7 +19,8 @@ repos:
         exclude: >
           (?x)^(
             cspell.json|
-            .*\.bib
+            .*\.bib|
+            .*\.svg
           )$
       - id: mixed-line-ending
       - id: name-tests-test
@@ -38,6 +39,9 @@ repos:
       - id: prettier
         language_version: 12.18.2 # prettier does not specify node correctly
 
+  # The following tools have to be install locally, because they can also be
+  # used by code editors (e.g. linting and format-on-save).
+
   - repo: local
     hooks:
       - id: black

.readthedocs.yml

@@ -11,5 +11,6 @@ formats:
 python:
   version: 3.7
   install:
+    - requirements: .reqs/doc.txt
     - method: pip
-      path: .[doc]
+      path: .

.reqs/dev.in

@@ -0,0 +1,10 @@
+-r ../requirements.txt
+-r doc.txt
+-r test.txt
+-r sty.txt
+
+jupyterlab
+jupyterlab-code-formatter
+labels
+pip-tools
+tox >= 1.9  # for skip_install, use_develop

.reqs/doc.in

@@ -0,0 +1,15 @@
+-r ../requirements.txt
+
+# Requirements to build documentation
+graphviz
+ipywidgets
+jupyter
+myst-nb
+pydeps
+Sphinx >= 3
+sphinx-book-theme
+sphinx-copybutton
+sphinx-panels
+sphinx-thebe
+sphinx-togglebutton
+sphobjinv

.reqs/doc.txt

@@ -0,0 +1,149 @@
+#
+# This file is autogenerated by pip-compile
+# To update, run:
+#
+#    pip-compile .reqs/doc.in
+#
+absl-py==0.11.0           # via -r .reqs/../requirements.txt, tensorboard, tensorflow
+alabaster==0.7.12         # via sphinx
+amplitf==0.0.1a2          # via -r .reqs/../requirements.txt
+argon2-cffi==20.1.0       # via notebook
+astunparse==1.6.3         # via -r .reqs/../requirements.txt, tensorflow
+async-generator==1.10     # via nbclient
+attrs==20.3.0             # via -r .reqs/../requirements.txt, expertsystem, jsonschema, jupyter-cache, markdown-it-py, particle, sphobjinv
+babel==2.9.0              # via sphinx
+backcall==0.2.0           # via ipython
+beautifulsoup4==4.9.3     # via sphinx-book-theme
+bleach==3.2.1             # via nbconvert
+cachetools==4.1.1         # via -r .reqs/../requirements.txt, google-auth
+certifi==2020.11.8        # via -r .reqs/../requirements.txt, requests, sphobjinv
+cffi==1.14.4              # via argon2-cffi
+chardet==3.0.4            # via -r .reqs/../requirements.txt, requests
+click==7.1.2              # via sphinx-book-theme
+cloudpickle==1.6.0        # via -r .reqs/../requirements.txt, tensorflow-probability
+colorama==0.4.4           # via nbdime
+decorator==4.4.2          # via -r .reqs/../requirements.txt, ipython, tensorflow-probability
+defusedxml==0.6.0         # via nbconvert
+dm-tree==0.1.5            # via -r .reqs/../requirements.txt, tensorflow-probability
+docutils==0.16            # via myst-nb, myst-parser, sphinx, sphinx-book-theme, sphinx-panels, sphinx-togglebutton
+entrypoints==0.3          # via nbconvert
+expertsystem==0.6.4       # via -r .reqs/../requirements.txt
+fuzzywuzzy==0.18.0        # via sphobjinv
+gast==0.3.3               # via -r .reqs/../requirements.txt, tensorflow, tensorflow-probability
+gitdb==4.0.5              # via gitpython
+gitpython==3.1.11         # via nbdime
+google-auth-oauthlib==0.4.2  # via -r .reqs/../requirements.txt, tensorboard
+google-auth==1.23.0       # via -r .reqs/../requirements.txt, google-auth-oauthlib, tensorboard
+google-pasta==0.2.0       # via -r .reqs/../requirements.txt, tensorflow
+graphviz==0.15            # via -r .reqs/doc.in
+grpcio==1.33.2            # via -r .reqs/../requirements.txt, tensorboard, tensorflow
+h5py==2.10.0              # via -r .reqs/../requirements.txt, tensorflow
+hepunits==2.0.1           # via -r .reqs/../requirements.txt, particle
+idna==2.10                # via -r .reqs/../requirements.txt, requests
+imagesize==1.2.0          # via sphinx
+iminuit==1.5.4            # via -r .reqs/../requirements.txt, amplitf
+importlib-metadata==3.1.0  # via myst-nb
+ipykernel==5.3.4          # via ipywidgets, jupyter, jupyter-console, notebook, qtconsole
+ipython-genutils==0.2.0   # via nbformat, notebook, qtconsole, traitlets
+ipython==7.19.0           # via ipykernel, ipywidgets, jupyter-console, jupyter-sphinx, myst-nb
+ipywidgets==7.5.1         # via -r .reqs/doc.in, jupyter, jupyter-sphinx, myst-nb
+jedi==0.17.2              # via ipython
+jinja2==2.11.2            # via nbconvert, nbdime, notebook, sphinx
+jsonschema==3.2.0         # via -r .reqs/../requirements.txt, expertsystem, nbformat, sphobjinv
+jupyter-cache==0.4.1      # via myst-nb
+jupyter-client==6.1.7     # via ipykernel, jupyter-console, nbclient, notebook, qtconsole
+jupyter-console==6.2.0    # via jupyter
+jupyter-core==4.7.0       # via jupyter-client, nbconvert, nbformat, notebook, qtconsole
+jupyter-sphinx==0.3.2     # via myst-nb
+jupyter==1.0.0            # via -r .reqs/doc.in
+keras-preprocessing==1.1.2  # via -r .reqs/../requirements.txt, tensorflow
+markdown-it-py==0.5.6     # via myst-parser
+markdown==3.3.3           # via -r .reqs/../requirements.txt, tensorboard
+markupsafe==1.1.1         # via jinja2
+mistune==0.8.4            # via nbconvert
+mpmath==1.1.0             # via -r .reqs/../requirements.txt, sympy
+myst-nb==0.10.1           # via -r .reqs/doc.in
+myst-parser==0.12.10      # via myst-nb
+nbclient==0.5.1           # via jupyter-cache
+nbconvert==5.6.1          # via jupyter, jupyter-sphinx, myst-nb, notebook
+nbdime==2.1.0             # via jupyter-cache
+nbformat==5.0.8           # via ipywidgets, jupyter-cache, jupyter-sphinx, myst-nb, nbclient, nbconvert, nbdime, notebook
+nest-asyncio==1.4.3       # via nbclient
+notebook==6.1.5           # via jupyter, nbdime, widgetsnbextension
+numpy==1.18.5             # via -r .reqs/../requirements.txt, amplitf, h5py, iminuit, keras-preprocessing, opt-einsum, pandas, tensorboard, tensorflow, tensorflow-probability
+oauthlib==3.1.0           # via -r .reqs/../requirements.txt, requests-oauthlib
+opt-einsum==3.3.0         # via -r .reqs/../requirements.txt, tensorflow
+packaging==20.4           # via bleach, sphinx
+pandas==1.1.4             # via -r .reqs/../requirements.txt
+pandocfilters==1.4.3      # via nbconvert
+parso==0.7.1              # via jedi
+particle==0.14.0          # via -r .reqs/../requirements.txt, expertsystem
+pexpect==4.8.0            # via ipython
+phasespace==1.2.0         # via -r .reqs/../requirements.txt
+pickleshare==0.7.5        # via ipython
+prometheus-client==0.9.0  # via notebook
+prompt-toolkit==3.0.8     # via ipython, jupyter-console
+protobuf==3.14.0          # via -r .reqs/../requirements.txt, tensorboard, tensorflow
+ptyprocess==0.6.0         # via pexpect, terminado
+pyasn1-modules==0.2.8     # via -r .reqs/../requirements.txt, google-auth
+pyasn1==0.4.8             # via -r .reqs/../requirements.txt, pyasn1-modules, rsa
+pycparser==2.20           # via cffi
+pydata-sphinx-theme==0.4.1  # via sphinx-book-theme
+pydeps==1.9.11            # via -r .reqs/doc.in
+pygments==2.7.2           # via ipython, jupyter-console, nbconvert, nbdime, qtconsole, sphinx
+pyparsing==2.4.7          # via packaging
+pyrsistent==0.17.3        # via -r .reqs/../requirements.txt, jsonschema
+python-constraint==1.4.0  # via -r .reqs/../requirements.txt, expertsystem
+python-dateutil==2.8.1    # via -r .reqs/../requirements.txt, jupyter-client, pandas
+pytz==2020.4              # via -r .reqs/../requirements.txt, babel, pandas
+pyyaml==5.3.1             # via -r .reqs/../requirements.txt, expertsystem, myst-nb, myst-parser, sphinx-book-theme
+pyzmq==20.0.0             # via jupyter-client, notebook, qtconsole
+qtconsole==5.0.1          # via jupyter
+qtpy==1.9.0               # via qtconsole
+requests-oauthlib==1.3.0  # via -r .reqs/../requirements.txt, google-auth-oauthlib
+requests==2.25.0          # via -r .reqs/../requirements.txt, nbdime, requests-oauthlib, sphinx, tensorboard
+rsa==4.6                  # via -r .reqs/../requirements.txt, google-auth
+send2trash==1.5.0         # via notebook
+six==1.15.0               # via -r .reqs/../requirements.txt, absl-py, argon2-cffi, astunparse, bleach, dm-tree, google-auth, google-pasta, grpcio, h5py, jsonschema, keras-preprocessing, nbdime, packaging, protobuf, python-dateutil, tensorboard, tensorflow, tensorflow-probability
+smmap==3.0.4              # via gitdb
+snowballstemmer==2.0.0    # via sphinx
+soupsieve==2.0.1          # via beautifulsoup4
+sphinx-book-theme==0.0.39  # via -r .reqs/doc.in
+sphinx-copybutton==0.3.1  # via -r .reqs/doc.in
+sphinx-panels==0.5.2      # via -r .reqs/doc.in
+sphinx-thebe==0.0.8       # via -r .reqs/doc.in
+sphinx-togglebutton==0.2.3  # via -r .reqs/doc.in, myst-nb
+sphinx==3.3.1             # via -r .reqs/doc.in, jupyter-sphinx, myst-nb, myst-parser, pydata-sphinx-theme, sphinx-book-theme, sphinx-copybutton, sphinx-panels, sphinx-thebe, sphinx-togglebutton
+sphinxcontrib-applehelp==1.0.2  # via sphinx
+sphinxcontrib-devhelp==1.0.2  # via sphinx
+sphinxcontrib-htmlhelp==1.0.3  # via sphinx
+sphinxcontrib-jsmath==1.0.1  # via sphinx
+sphinxcontrib-qthelp==1.0.3  # via sphinx
+sphinxcontrib-serializinghtml==1.1.4  # via sphinx
+sphobjinv==2.0.1          # via -r .reqs/doc.in
+sqlalchemy==1.3.20        # via jupyter-cache
+stdlib-list==0.8.0        # via pydeps
+sympy==1.6.2              # via -r .reqs/../requirements.txt, amplitf
+tensorboard-plugin-wit==1.7.0  # via -r .reqs/../requirements.txt, tensorboard
+tensorboard==2.4.0        # via -r .reqs/../requirements.txt, tensorflow
+tensorflow-estimator==2.3.0  # via -r .reqs/../requirements.txt, tensorflow
+tensorflow-probability==0.11.1  # via -r .reqs/../requirements.txt, phasespace
+tensorflow==2.3.1         # via -r .reqs/../requirements.txt, amplitf, phasespace
+termcolor==1.1.0          # via -r .reqs/../requirements.txt, tensorflow
+terminado==0.9.1          # via notebook
+testpath==0.4.4           # via nbconvert
+tornado==6.1              # via ipykernel, jupyter-client, nbdime, notebook, terminado
+tqdm==4.53.0              # via -r .reqs/../requirements.txt, expertsystem
+traitlets==5.0.5          # via ipykernel, ipython, ipywidgets, jupyter-client, jupyter-core, nbclient, nbconvert, nbformat, notebook, qtconsole
+urllib3==1.26.2           # via -r .reqs/../requirements.txt, requests
+wcwidth==0.2.5            # via prompt-toolkit
+webencodings==0.5.1       # via bleach
+werkzeug==1.0.1           # via -r .reqs/../requirements.txt, tensorboard
+wheel==0.35.1             # via -r .reqs/../requirements.txt, astunparse, sphinx-togglebutton, tensorboard, tensorflow
+widgetsnbextension==3.5.1  # via ipywidgets
+wrapt==1.12.1             # via -r .reqs/../requirements.txt, tensorflow
+xmltodict==0.12.0         # via -r .reqs/../requirements.txt, expertsystem
+zipp==3.4.0               # via importlib-metadata
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools

.reqs/sty.in

@@ -0,0 +1,24 @@
+-r ../requirements.txt
+-r test.txt  # for pytest type hints
+
+pre-commit >= 1.4.0
+
+# Requirements for formatting files
+black
+isort
+nbstripout
+
+# Lint Python source code
+flake8  >= 3  # for per-file-ignores
+flake8-blind-except
+flake8-bugbear
+flake8-builtins
+flake8-rst-docstrings
+mypy
+pep8-naming
+pydocstyle
+pylint
+
+# Lint documentation files
+doc8
+rstcheck