update and reduce environment files

Author: OriolAbril

.pre-commit-config.yaml

@@ -52,7 +52,7 @@ repos:
     - id: pip-from-conda
       additional_dependencies: [pyyaml]
       entry: python scripts/generate_pip_deps_from_conda.py
-      files: ^conda-envs/
+      files: ^conda-envs/environment-dev-py.+.yml$
       language: python
       name: Generate pip dependency from conda
     - id: no-relative-imports

conda-envs/environment-dev-py37.yml

@@ -1,3 +1,4 @@
+# "dev" conda envs are to be used by devs in setting their local environments
 name: pymc-dev-py37
 channels:
 - conda-forge
@@ -8,7 +9,7 @@ dependencies:
 - cachetools>=4.2.1
 - cloudpickle
 - fastprogress>=0.2.0
-- h5py
+- h5py>=2.7
 - ipython
 - myst-nb
 - numpy>=1.15
@@ -20,13 +21,11 @@ dependencies:
 - pytest>=3.0
 - python-graphviz
 - python=3.7
-- recommonmark>=0.4
 - scipy>1.4.1
 - sphinx-autobuild>=0.7
 - sphinx-notfound-page
 - sphinx-panels
 - sphinx>=1.5
 - typing-extensions
-- watermark
 - pip:
   - sphinx-design

conda-envs/environment-dev-py38.yml

@@ -1,3 +1,4 @@
+# "dev" conda envs are to be used by devs in setting their local environments
 name: pymc-dev-py38
 channels:
 - conda-forge
@@ -8,7 +9,7 @@ dependencies:
 - cachetools>=4.2.1
 - cloudpickle
 - fastprogress>=0.2.0
-- h5py
+- h5py>=2.7
 - ipython
 - myst-nb
 - numpy>=1.15.0
@@ -20,13 +21,11 @@ dependencies:
 - pytest>=3.0
 - python-graphviz
 - python=3.8
-- recommonmark>=0.4
 - scipy>1.4.1
 - sphinx-autobuild>=0.7
 - sphinx-notfound-page
 - sphinx-panels
 - sphinx>=1.5
 - typing-extensions>=3.7.4
-- watermark
 - pip:
   - sphinx-design

conda-envs/environment-dev-py39.yml

@@ -1,3 +1,4 @@
+# "dev" conda envs are to be used by devs in setting their local environments
 name: pymc-dev-py39
 channels:
 - conda-forge
@@ -20,13 +21,11 @@ dependencies:
 - pytest>=3.0
 - python-graphviz
 - python=3.9
-- recommonmark>=0.4
 - scipy>1.4.1
 - sphinx-autobuild>=0.7
 - sphinx-notfound-page
 - sphinx-panels
 - sphinx>=1.5
 - typing-extensions>=3.7.4
-- watermark
 - pip:
   - sphinx-design

conda-envs/environment-test-py37.yml

@@ -1,3 +1,4 @@
+# "test" conda envs are used to set up our CI environment in GitHub actions
 name: pymc-test-py37
 channels:
 - conda-forge
@@ -12,23 +13,12 @@ dependencies:
 - ipython
 - libblas=*=*mkl
 - mkl-service
-- myst-nb
 - numpy>=1.15.0
-- numpydoc>=0.9
 - pandas=0.24
 - pre-commit>=2.8.0
-- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.7
-- recommonmark>=0.4
 - scipy>1.4.1
-- sphinx-autobuild>=0.7
-- sphinx-notfound-page
-- sphinx-panels
-- sphinx>=1.5
 - typing-extensions
-- watermark
-- pip:
-  - sphinx-design

conda-envs/environment-test-py38.yml

@@ -1,3 +1,4 @@
+# "test" conda envs are used to set up our CI environment in GitHub actions
 name: pymc-test-py38
 channels:
 - conda-forge
@@ -12,24 +13,12 @@ dependencies:
 - ipython
 - libblas=*=*mkl
 - mkl-service
-- myst-nb
-- nbsphinx>=0.4
 - numpy>=1.15.0
-- numpydoc>=0.9
 - pandas
 - pre-commit>=2.8.0
-- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.8
-- recommonmark>=0.4
 - scipy>1.4.1
-- sphinx-autobuild>=0.7
-- sphinx-notfound-page
-- sphinx-panels
-- sphinx>=1.5
 - typing-extensions>=3.7.4
-- watermark
-- pip:
-  - sphinx-design

conda-envs/environment-test-py39.yml

@@ -1,3 +1,4 @@
+# "test" conda envs are used to set up our CI environment in GitHub actions
 name: pymc-test-py39
 channels:
 - conda-forge
@@ -12,24 +13,12 @@ dependencies:
 - ipython>=7.16
 - libblas=*=*mkl
 - mkl-service
-- myst-nb
-- nbsphinx>=0.4
 - numpy>=1.15.0
-- numpydoc>=0.9
 - pandas
 - pre-commit>=2.8.0
-- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
 - python=3.9
-- recommonmark>=0.4
 - scipy>1.4.1
-- sphinx-autobuild>=0.7
-- sphinx-notfound-page
-- sphinx-panels
-- sphinx>=1.5
 - typing-extensions>=3.7.4
-- watermark
-- pip:
-  - sphinx-design

conda-envs/windows-environment-dev-py38.yml

@@ -25,7 +25,6 @@ dependencies:
 - pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
-- recommonmark>=0.4
 - sphinx-autobuild>=0.7
 - sphinx-notfound-page
 - sphinx-panels

conda-envs/windows-environment-test-py38.yml

@@ -20,17 +20,8 @@ dependencies:
 - python-graphviz
 - scipy>1.4.1
 - typing-extensions>=3.7.4
-# Extra stuff for dev, testing and docs build
+# Extra stuff for testing
 - ipython>=7.16
-- myst-nb
-- nbsphinx>=0.4
-- numpydoc>=0.9
 - pre-commit>=2.8.0
-- pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
-- recommonmark>=0.4
-- sphinx-autobuild>=0.7
-- sphinx-panels
-- sphinx>=1.5
-- watermark

requirements-dev.txt

@@ -6,7 +6,7 @@ arviz>=0.11.4
 cachetools>=4.2.1
 cloudpickle
 fastprogress>=0.2.0
-h5py
+h5py>=2.7
 ipython
 myst-nb
 numpy>=1.15.0
@@ -16,12 +16,10 @@ pre-commit>=2.8.0
 pydata-sphinx-theme
 pytest-cov>=2.5
 pytest>=3.0
-recommonmark>=0.4
 scipy>1.4.1
 sphinx-autobuild>=0.7
 sphinx-design
 sphinx-notfound-page
 sphinx-panels
 sphinx>=1.5
 typing-extensions>=3.7.4
-watermark