Align conda envs and add Windows 3.9 env (#5895)

* Remove conda sorter from `pre-commit` config

Author: hectormz

.pre-commit-config.yaml

@@ -57,8 +57,6 @@ repos:
   hooks:
     - id: no-print-statements
       files: ^pymc/
-    - id: conda-env-sorter
-      files: ^conda-envs/environment-dev-py.+\.yml$
 - repo: local
   hooks:
     - id: check-no-tests-are-ignored

conda-envs/environment-dev-py37.yml

@@ -4,6 +4,7 @@ channels:
 - conda-forge
 - defaults
 dependencies:
+# Base dependencies
 - aeppl=0.0.31
 - aesara=2.7.2
 - arviz>=0.12.0
@@ -12,26 +13,27 @@ dependencies:
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py>=2.7
+- numpy>=1.15.0
+- pandas>=0.24.0
+- pip
+- python=3.7
+- python-graphviz
+- scipy>=1.4.1
+- typing-extensions>=3.7.4
+# Extra dependencies for dev, testing and docs build
 - ipython>=7.16
 - jax
 - jupyter-sphinx
 - myst-nb
-- numpy>=1.15.0
 - numpydoc
-- pandas>=0.24.0
-- pip
 - pre-commit>=2.8.0
 - pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
-- python-graphviz
-- python=3.7
-- scipy>=1.4.1
 - sphinx-copybutton
 - sphinx-notfound-page
 - sphinx>=1.5
 - sphinxext-rediraffe
-- typing-extensions>=3.7.4
 - watermark
 - pip:
   - polyagamma

conda-envs/environment-dev-py38.yml

@@ -4,6 +4,7 @@ channels:
 - conda-forge
 - defaults
 dependencies:
+# Base dependencies
 - aeppl=0.0.31
 - aesara=2.7.2
 - arviz>=0.12.0
@@ -12,26 +13,27 @@ dependencies:
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py>=2.7
+- numpy>=1.15.0
+- pandas>=0.24.0
+- pip
+- python=3.8
+- python-graphviz
+- scipy>=1.4.1
+- typing-extensions>=3.7.4
+# Extra dependencies for dev, testing and docs build
 - ipython>=7.16
 - jax
 - jupyter-sphinx
 - myst-nb
-- numpy>=1.15.0
 - numpydoc
-- pandas>=0.24.0
-- pip
 - pre-commit>=2.8.0
 - pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
-- python-graphviz
-- python=3.8
-- scipy>=1.4.1
 - sphinx-copybutton
 - sphinx-notfound-page
 - sphinx>=1.5
 - sphinxext-rediraffe
-- typing-extensions>=3.7.4
 - watermark
 - pip:
   - polyagamma

conda-envs/environment-dev-py39.yml

@@ -4,6 +4,7 @@ channels:
 - conda-forge
 - defaults
 dependencies:
+# Base dependencies
 - aeppl=0.0.31
 - aesara=2.7.2
 - arviz>=0.12.0
@@ -12,26 +13,27 @@ dependencies:
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py>=2.7
+- numpy>=1.15.0
+- pandas>=0.24.0
+- pip
+- python=3.9
+- python-graphviz
+- scipy>=1.4.1
+- typing-extensions>=3.7.4
+# Extra dependencies for dev, testing and docs build
 - ipython>=7.16
 - jax
 - jupyter-sphinx
 - myst-nb
-- numpy>=1.15.0
 - numpydoc
-- pandas>=0.24.0
-- pip
 - pre-commit>=2.8.0
 - pydata-sphinx-theme
 - pytest-cov>=2.5
 - pytest>=3.0
-- python-graphviz
-- python=3.9
-- scipy>=1.4.1
 - sphinx-copybutton
 - sphinx-notfound-page
 - sphinx>=1.5
 - sphinxext-rediraffe
-- typing-extensions>=3.7.4
 - watermark
 - pip:
   - polyagamma

conda-envs/environment-test-py37.yml

@@ -4,6 +4,7 @@ channels:
 - conda-forge
 - defaults
 dependencies:
+# Base dependencies
 - aeppl=0.0.31
 - aesara=2.7.2
 - arviz>=0.12.0
@@ -12,16 +13,17 @@ dependencies:
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py>=2.7
-- ipython>=7.16
 - jax
 - libblas=*=*mkl
 - mkl-service
 - numpy>=1.15.0
 - pandas>=0.24.0
-- pre-commit>=2.8.0
-- pytest-cov>=2.5
-- pytest>=3.0
-- python-graphviz
 - python=3.7
+- python-graphviz
 - scipy>=1.4.1
 - typing-extensions>=3.7.4
+# Extra dependencies for testing
+- ipython>=7.16
+- pre-commit>=2.8.0
+- pytest-cov>=2.5
+- pytest>=3.0

conda-envs/environment-test-py38.yml

@@ -4,6 +4,7 @@ channels:
 - conda-forge
 - defaults
 dependencies:
+# Base dependencies
 - aeppl=0.0.31
 - aesara=2.7.2
 - arviz>=0.12.0
@@ -12,16 +13,17 @@ dependencies:
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py>=2.7
-- ipython>=7.16
 - jax
 - libblas=*=*mkl
 - mkl-service
 - numpy>=1.15.0
 - pandas>=0.24.0
-- pre-commit>=2.8.0
-- pytest-cov>=2.5
-- pytest>=3.0
-- python-graphviz
 - python=3.8
+- python-graphviz
 - scipy>=1.4.1
 - typing-extensions>=3.7.4
+# Extra dependencies for testing
+- ipython>=7.16
+- pre-commit>=2.8.0
+- pytest-cov>=2.5
+- pytest>=3.0

conda-envs/environment-test-py39.yml

@@ -4,6 +4,7 @@ channels:
 - conda-forge
 - defaults
 dependencies:
+# Base dependencies
 - aeppl=0.0.31
 - aesara=2.7.2
 - arviz>=0.12.0
@@ -12,16 +13,17 @@ dependencies:
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py>=2.7
-- ipython>=7.16
 - jax
 - libblas=*=*mkl
 - mkl-service
 - numpy>=1.15.0
 - pandas>=0.24.0
-- pre-commit>=2.8.0
-- pytest-cov>=2.5
-- pytest>=3.0
-- python-graphviz
 - python=3.9
+- python-graphviz
 - scipy>=1.4.1
 - typing-extensions>=3.7.4
+# Extra dependencies for testing
+- ipython>=7.16
+- pre-commit>=2.8.0
+- pytest-cov>=2.5
+- pytest>=3.0

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

@@ -1,9 +1,10 @@
+# "dev" conda envs are to be used by devs in setting their local environments
 name: pymc-dev-py38
 channels:
 - conda-forge
 - defaults
 dependencies:
- # base dependencies (see install guide for Windows)
+# Base dependencies (see install guide for Windows)
 - aeppl=0.0.31
 - aesara=2.7.2
 - arviz>=0.12.0
@@ -20,7 +21,7 @@ dependencies:
 - python-graphviz
 - scipy>=1.4.1
 - typing-extensions>=3.7.4
-# Extra stuff for dev, testing and docs build
+# Extra dependencies for dev, testing and docs build
 - ipython>=7.16
 - myst-nb
 - numpydoc

conda-envs/windows-environment-dev-py39.yml

@@ -0,0 +1,38 @@
+# "dev" conda envs are to be used by devs in setting their local environments
+name: pymc-dev-py39
+channels:
+- conda-forge
+- defaults
+dependencies:
+# Base dependencies (see install guide for Windows)
+- aeppl=0.0.31
+- aesara=2.6.6
+- arviz>=0.12.0
+- blas
+- cachetools>=4.2.1
+- cloudpickle
+- fastprogress>=0.2.0
+- h5py>=2.7
+- numpy>=1.15.0
+- pandas>=0.24.0
+- pip
+- python=3.9
+- python-graphviz
+- scipy>=1.4.1
+- typing-extensions>=3.7.4
+# Extra dependencies for dev, testing and docs build
+- ipython>=7.16
+- myst-nb
+- numpydoc
+- pre-commit>=2.8.0
+- pydata-sphinx-theme
+- pytest-cov>=2.5
+- pytest>=3.0
+- sphinx-autobuild>=0.7
+- sphinx-copybutton
+- sphinx-notfound-page
+- sphinx>=1.5
+- watermark
+- pip:
+  - sphinx-design
+  - sphinx-remove-toctrees

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

@@ -1,9 +1,10 @@
+# "test" conda envs are used to set up our CI environment in GitHub actions
 name: pymc-test-py38
 channels:
 - conda-forge
 - defaults
 dependencies:
- # base dependencies (see install guide for Windows)
+# Base dependencies (see install guide for Windows)
 - aeppl=0.0.31
 - aesara=2.7.2
 - arviz>=0.12.0
@@ -23,7 +24,7 @@ dependencies:
 - python-graphviz
 - scipy>=1.4.1
 - typing-extensions>=3.7.4
-# Extra stuff for testing
+# Extra dependencies for testing
 - ipython>=7.16
 - pre-commit>=2.8.0
 - pytest-cov>=2.5

conda-envs/windows-environment-test-py39.yml

@@ -0,0 +1,31 @@
+# "test" conda envs are used to set up our CI environment in GitHub actions
+name: pymc-test-py39
+channels:
+- conda-forge
+- defaults
+dependencies:
+# Base dependencies (see install guide for Windows)
+- aeppl=0.0.31
+- aesara=2.6.6
+- arviz>=0.12.0
+- blas
+- cachetools>=4.2.1
+- cloudpickle
+- fastprogress>=0.2.0
+- h5py>=2.7
+- libpython
+- mkl==2020.4
+- mkl-service==2.3.0
+- m2w64-toolchain
+- numpy>=1.15.0
+- pandas>=0.24.0
+- pip
+- python=3.9
+- python-graphviz
+- scipy>=1.4.1
+- typing-extensions>=3.7.4
+# Extra dependencies for testing
+- ipython>=7.16
+- pre-commit>=2.8.0
+- pytest-cov>=2.5
+- pytest>=3.0

scripts/generate_pip_deps_from_conda.py

@@ -126,12 +126,12 @@ def main(conda_fname, pip_fname):
             raise ValueError(f"Unexpected dependency {dep}")
 
     header = (
-        f"# This file is auto-generated by scripts/generate_pip_deps_from_conda.py, "
+        "# This file is auto-generated by scripts/generate_pip_deps_from_conda.py, "
         "do not modify.\n# See that file for comments about the need/usage of each dependency.\n\n"
     )
     pip_content = header + "\n".join(sorted(pip_deps)) + "\n"
 
-    with open(pip_fname, "w") as pip_fd:
+    with open(pip_fname, "w", newline="") as pip_fd:
         pip_fd.write(pip_content)