Fix dependencies in requirements-dev.txt (#5070)

* Fix dependencies in requirements-dev.txt

* Fix dependencies in conda files

* Fix pre-commit one more time

* update and reduce environment files

* unpin pandas

Co-authored-by: Oriol (ZBook) <[email protected]>

Author: Sayam753

.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

@@ -1,31 +1,24 @@
+# "test" conda envs are used to set up our CI environment in GitHub actions
 name: pymc-test-py37
 channels:
 - conda-forge
 - defaults
 dependencies:
 - aesara>=2.1.0
-- arviz>=0.11.2
+- arviz>=0.11.4
 - cachetools>=4.2.1
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py>=2.7
 - ipython
 - libblas=*=*mkl
 - mkl-service
-- myst-nb
 - numpy>=1.15.0
-- numpydoc>=0.9
-- pandas=0.24
+- 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-panels
-- sphinx>=1.5
 - typing-extensions
-- watermark

conda-envs/environment-test-py38.yml

@@ -1,32 +1,24 @@
+# "test" conda envs are used to set up our CI environment in GitHub actions
 name: pymc-test-py38
 channels:
 - conda-forge
 - defaults
 dependencies:
 - aesara>=2.1.0
-- arviz>=0.11.2
+- arviz>=0.11.4
 - cachetools>=4.2.1
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py>=2.7
 - 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-panels
-- sphinx>=1.5
 - typing-extensions>=3.7.4
-- watermark

conda-envs/environment-test-py39.yml

@@ -1,32 +1,24 @@
+# "test" conda envs are used to set up our CI environment in GitHub actions
 name: pymc-test-py39
 channels:
 - conda-forge
 - defaults
 dependencies:
 - aesara>=2.1.0
-- arviz>=0.11.2
+- arviz>=0.11.4
 - cachetools
 - cloudpickle
 - fastprogress>=0.2.0
 - h5py
 - 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-panels
-- sphinx>=1.5
 - typing-extensions>=3.7.4
-- watermark

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

@@ -2,25 +2,24 @@
 # See that file for comments about the need/usage of each dependency.
 
 aesara>=2.1.0
-arviz>=0.11.2
-cachetools
+arviz>=0.11.4
+cachetools>=4.2.1
 cloudpickle
 fastprogress>=0.2.0
 h5py>=2.7
-ipython>=7.16
+ipython
 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
-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