Rename to pymc-extras (#404)

Co-authored-by: Ricardo Vieira <[email protected]>

Author: fonnesbeck

.gitattributes

@@ -1 +1 @@
-pymc_experimental/_version.py export-subst
+pymc_extras/_version.py export-subst

.github/workflows/pypi.yml

@@ -28,18 +28,18 @@ jobs:
             cd test-sdist
             python -m venv venv-sdist
             venv-sdist/bin/python -m pip install numpy
-            venv-sdist/bin/python -m pip install ../dist/pymc_experimental*.tar.gz
+            venv-sdist/bin/python -m pip install ../dist/pymc_extras*.tar.gz
             echo "Checking import and version number (on release)"
-            venv-sdist/bin/python -c "import pymc_experimental as pmx; assert pmx.__version__ == '${{ github.ref_name }}'[1:] if '${{ github.ref_type }}' == 'tag' else True; print(pmx.__version__)"
+            venv-sdist/bin/python -c "import pymc_extras as pmx; assert pmx.__version__ == '${{ github.ref_name }}'[1:] if '${{ github.ref_type }}' == 'tag' else True; print(pmx.__version__)"
             cd ..
       - name: Check the bdist installs and imports
         run: |
               mkdir -p test-bdist
               cd test-bdist
               python -m venv venv-bdist
-              venv-bdist/bin/python -m pip install ../dist/pymc_experimental*.whl
+              venv-bdist/bin/python -m pip install ../dist/pymc_extras*.whl
               echo "Checking import and version number (on release)"
-              venv-bdist/bin/python -c "import pymc_experimental as pmx; assert pmx.__version__ == '${{ github.ref_name }}'[1:] if '${{ github.ref_type }}' == 'tag' else pmx.__version__; print(pmx.__version__)"
+              venv-bdist/bin/python -c "import pymc_extras as pmx; assert pmx.__version__ == '${{ github.ref_name }}'[1:] if '${{ github.ref_type }}' == 'tag' else pmx.__version__; print(pmx.__version__)"
               cd ..
       - uses: actions/upload-artifact@v3
         with:

.github/workflows/test.yml

@@ -6,7 +6,7 @@ on:
     branches: [main]
     paths:
       - ".github/workflows/*"
-      - "pymc_experimental/**"
+      - "pymc_extras/**"
       - "tests/**"
       - "setup.py"
       - "pyproject.toml"
@@ -37,16 +37,16 @@ jobs:
           environment-file: conda-envs/environment-test.yml
           create-args: >-
             python=${{matrix.python-version}}
-          environment-name: pymc-experimental-test
+          environment-name: pymc-extras-test
           init-shell: bash
           cache-environment: true
-      - name: Install pymc-experimental
+      - name: Install pymc-extras
         run: |
           pip install -e .
           python --version
       - name: Run tests
         run: |
-          python -m pytest -vv --cov=pymc_experimental --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
+          python -m pytest -vv --cov=pymc_extras --cov-append --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v2
         with:
@@ -76,18 +76,18 @@ jobs:
           micromamba-version: "1.5.10-0"  # Until https://github.com/mamba-org/mamba/issues/3467 is not fixed
           create-args: >-
             python=${{matrix.python-version}}
-          environment-name: pymc-experimental-test
+          environment-name: pymc-extras-test
           init-shell: cmd.exe
           cache-environment: true
-      - name: Install pymc-experimental
+      - name: Install pymc-extras
         run: |
           pip install -e .
           python --version
       - name: Run tests
         # This job uses a cmd shell, therefore the environment variable syntax is different!
         # The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
         run: >-
-          python -m pytest -vv --cov=pymc_experimental --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
+          python -m pytest -vv --cov=pymc_extras --cov-append --cov-report=xml --cov-report term --durations=50 %TEST_SUBSET%
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v2
         with:

.gitpod.yml

@@ -3,14 +3,14 @@ tasks:
   - name: initialize
     init: |
       mkdir -p .vscode
-      echo '{"python.defaultInterpreterPath": "/workspace/pymc-experimental/env/bin/python"}' > .vscode/settings.json
+      echo '{"python.defaultInterpreterPath": "/workspace/pymc-extras/env/bin/python"}' > .vscode/settings.json
       conda init bash && source ~/.bashrc
       conda env update -f conda-envs/environment-test.yml -p env
-      conda activate /workspace/pymc-experimental/env
+      conda activate /workspace/pymc-extras/env
       pip install -r requirements-dev.txt
       pip install -e .
     command: |
-      conda init bash && echo "conda activate /workspace/pymc-experimental/env" >> ~/.bashrc && source ~/.bashrc
+      conda init bash && echo "conda activate /workspace/pymc-extras/env" >> ~/.bashrc && source ~/.bashrc
 
 vscode:
   extensions:

.pre-commit-config.yaml

@@ -27,4 +27,4 @@ repos:
   hooks:
     - id: no-print-statements
       exclude: _version.py
-      files: ^pymc_experimental/
+      files: ^pymc_extras/

CONTRIBUTING.md

@@ -1,3 +1,3 @@
 # Contributing guide
 
-Page in construction, for now go to https://github.com/pymc-devs/pymc-experimental#questions.
+Page in construction, for now go to https://github.com/pymc-devs/pymc-extras#questions.

MANIFEST.in

@@ -1,4 +1,5 @@
 include requirements*.txt
 include *.md *.rst
 include LICENSE
-include pymc_experimental/version.txt
+include README.md
+include pymc_extras/version.txt

README.md

@@ -1,29 +1,29 @@
-# Welcome to `pymc-experimental`
-<a href="https://gitpod.io/#https://github.com/pymc-devs/pymc-experimental">
+# Welcome to `pymc-extras`
+<a href="https://gitpod.io/#https://github.com/pymc-devs/pymc-extras">
   <img
     src="https://img.shields.io/badge/Contribute%20with-Gitpod-908a85?logo=gitpod"
     alt="Contribute with Gitpod"
   />
 </a>
 <img
-  src="https://codecov.io/gh/pymc-devs/pymc-experimental/branch/main/graph/badge.svg"
+  src="https://codecov.io/gh/pymc-devs/pymc-extras/branch/main/graph/badge.svg"
   alt="Codecov Badge"
 />
 
 As PyMC continues to mature and expand its functionality to accommodate more domains of application, we increasingly see cutting-edge methodologies, highly specialized statistical distributions, and complex models appear.
 While this adds to the functionality and relevance of the project, it can also introduce instability and impose a burden on testing and quality control.
-To reduce the burden on the main `pymc` repository, this `pymc-experimental` repository can become the aggregator and testing ground for new additions to PyMC.
+To reduce the burden on the main `pymc` repository, this `pymc-extras` repository can become the aggregator and testing ground for new additions to PyMC.
 This may include unusual probability distributions, advanced model fitting algorithms, innovative yet not fully tested methods or any code that may be inappropriate to include in the `pymc` repository, but may want to be made available to users.
 
-The `pymc-experimental` repository can be understood as the first step in the PyMC development pipeline, where all novel code is introduced until it is obvious that it belongs in the main repository.
+The `pymc-extras` repository can be understood as the first step in the PyMC development pipeline, where all novel code is introduced until it is obvious that it belongs in the main repository.
 We hope that this organization improves the stability and streamlines the testing overhead of the `pymc` repository, while allowing users and developers to test and evaluate cutting-edge methods and not yet fully mature features.
 
-`pymc-experimental` would be designed to mirror the namespaces in `pymc` to make usage and migration as easy as possible.
+`pymc-extras` would be designed to mirror the namespaces in `pymc` to make usage and migration as easy as possible.
 For example, a `ParabolicFractal` distribution could be used analogously to those in `pymc`:
 
 ```python
 import pymc as pm
-import pymc_experimental as pmx
+import pymc_extras as pmx
 
 with pm.Model():
 
@@ -35,23 +35,23 @@ with pm.Model():
 
 ## Questions
 
-### What belongs in `pymc-experimental`?
+### What belongs in `pymc-extras`?
 
 - newly-implemented statistical methods, for example step methods or model construction helpers
 - distributions that are tricky to sample from or test
 - infrequently-used fitting methods or distributions
 - any code that requires additional optimization before it can be used in practice
 
 
-### What does not belong in `pymc-experimental`?
+### What does not belong in `pymc-extras`?
 - Case studies
 - Implementations that cannot be applied generically, for example because they are tied to variables from a toy example
 
 
 ### Should there be more than one add-on repository?
 
 Since there is a lot of code that we may not want in the main repository, does it make sense to have more than one additional repository?
-For example, `pymc-experimental` may just include methods that are not fully developed, tested and trusted, while code that is known to work well and has adequate test coverage, but is still too specialized to become part of `pymc` could reside in a `pymc-extras` (or similar) repository.
+For example, `pymc-extras` may just include methods that are not fully developed, tested and trusted, while code that is known to work well and has adequate test coverage, but is still too specialized to become part of `pymc` could reside in a `pymc-extras` (or similar) repository.
 
 
 ### Unanswered questions & ToDos

conda-envs/environment-test.yml

@@ -1,4 +1,4 @@
-name: pymc-experimental-test
+name: pymc-extras-test
 channels:
 - conda-forge
 - nodefaults

conda-envs/windows-environment-test.yml

@@ -1,4 +1,4 @@
-name: pymc-experimental-test
+name: pymc-extras-test
 channels:
 - conda-forge
 - defaults

docs/api_reference.rst

@@ -7,7 +7,7 @@ Model
 This reference provides detailed documentation for all modules, classes, and
 methods in the current release of PyMC experimental.
 
-.. currentmodule:: pymc_experimental
+.. currentmodule:: pymc_extras
 .. autosummary::
    :toctree: generated/
 
@@ -19,7 +19,7 @@ methods in the current release of PyMC experimental.
 Inference
 =========
 
-.. currentmodule:: pymc_experimental.inference
+.. currentmodule:: pymc_extras.inference
 .. autosummary::
    :toctree: generated/
 
@@ -29,7 +29,7 @@ Inference
 Distributions
 =============
 
-.. currentmodule:: pymc_experimental.distributions
+.. currentmodule:: pymc_extras.distributions
 .. autosummary::
    :toctree: generated/
 
@@ -47,7 +47,7 @@ Distributions
 Utils
 =====
 
-.. currentmodule:: pymc_experimental.utils
+.. currentmodule:: pymc_extras.utils
 .. autosummary::
    :toctree: generated/
 
@@ -57,7 +57,7 @@ Utils
 
 Statespace Models
 =================
-.. automodule:: pymc_experimental.statespace
+.. automodule:: pymc_extras.statespace
 .. toctree::
    :maxdepth: 1
 
@@ -68,7 +68,7 @@ Statespace Models
 
 Model Transforms
 ================
-.. automodule:: pymc_experimental.model.transforms
+.. automodule:: pymc_extras.model.transforms
 .. autosummary::
    :toctree: generated/
 
@@ -78,7 +78,7 @@ Model Transforms
 
 Printing
 ========
-.. currentmodule:: pymc_experimental.printing
+.. currentmodule:: pymc_extras.printing
 .. autosummary::
    :toctree: generated/
 

docs/conf.py

@@ -29,18 +29,18 @@
 import os
 import sys
 
-import pymc_experimental  # isort:skip
+import pymc_extras  # isort:skip
 
 sys.path.insert(0, os.path.abspath("../"))
 
 # -- Project information -----------------------------------------------------
 
-project = "pymc_experimental"
+project = "pymc_extras"
 copyright = "2022, pymc-devs"
 author = "pymc-devs"
 
 # The short X.Y version
-version = pymc_experimental.__version__
+version = pymc_extras.__version__
 # The full version, including alpha/beta/rc tags
 release = version
 
@@ -118,7 +118,7 @@
 }
 html_context = {
     "github_user": "pymc-devs",
-    "github_repo": "pymc-experimental",
+    "github_repo": "pymc-extras",
     "github_version": "main",
     "doc_path": "docs",
     "default_mode": "light",
@@ -133,7 +133,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "pymc_experimentaldoc"
+htmlhelp_basename = "pymc_extrasdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -159,9 +159,9 @@
 latex_documents = [
     (
         master_doc,
-        "pymc_experimental.tex",
-        "pymc_experimental Documentation",
-        "The developers of pymc_experimental",
+        "pymc_extras.tex",
+        "pymc_extras Documentation",
+        "The developers of pymc_extras",
         "manual",
     ),
 ]
@@ -171,7 +171,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "pymc_experimental", "pymc_experimental Documentation", [author], 1)]
+man_pages = [(master_doc, "pymc_extras", "pymc_extras Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -182,10 +182,10 @@
 texinfo_documents = [
     (
         master_doc,
-        "pymc_experimental",
-        "pymc_experimental Documentation",
+        "pymc_extras",
+        "pymc_extras Documentation",
         author,
-        "pymc_experimental",
+        "pymc_extras",
         "One line description of project.",
         "Miscellaneous",
     ),

docs/index.rst

@@ -1,15 +1,15 @@
-PyMC experimental
+PyMC Extras
 ===================================================
 |Tests|
 |Coverage|
 |Black|
 
 
-.. |Tests| image:: https://github.com/pymc-devs/pymc-experimental/actions/workflows/test.yml/badge.svg
-    :target: https://github.com/pymc-devs/pymc-experimental
+.. |Tests| image:: https://github.com/pymc-devs/pymc-extras/actions/workflows/test.yml/badge.svg
+    :target: https://github.com/pymc-devs/pymc-extras
 
-.. |Coverage| image:: https://codecov.io/gh/pymc-devs/pymc-experimental/branch/main/graph/badge.svg?token=ZqH0KCLKAE
-    :target: https://codecov.io/gh/pymc-devs/pymc-experimental
+.. |Coverage| image:: https://codecov.io/gh/pymc-devs/pymc-extras/branch/main/graph/badge.svg?token=ZqH0KCLKAE
+    :target: https://codecov.io/gh/pymc-devs/pymc-extras
 
 .. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
     :target: https://github.com/ambv/black
@@ -21,25 +21,25 @@ Where we grow the next batch of cool PyMC features
 Installation
 ============
 
-To install the latest release on [PyPI](https://pypi.org/project/pymc-experimental/), you can use a package manager like pip:
+To install the latest release on [PyPI](https://pypi.org/project/pymc-extras/), you can use a package manager like pip:
 
 .. code-block:: bash
 
-   pip install pymc-experimental
+   pip install pymc-extras
 
 For the development version, you can install directly from GitHub:
 
 .. code-block:: bash
 
-  pip install git+https://github.com/pymc-devs/pymc-experimental.git
+  pip install git+https://github.com/pymc-devs/pymc-extras.git
 
 Contributing
 ============
-We welcome contributions from interested individuals or groups! For information about contributing to PyMC experimental check out our instructions, policies, and guidelines `here <https://github.com/pymc-devs/pymc-experimental/blob/main/CONTRIBUTING.md>`_.
+We welcome contributions from interested individuals or groups! For information about contributing to PyMC Extras check out our instructions, policies, and guidelines `here <https://github.com/pymc-devs/pymc-extras/blob/main/CONTRIBUTING.md>`_.
 
 Contributors
 ============
-See the `GitHub contributor page <https://github.com/pymc-devs/pymc-experimental/graphs/contributors>`_.
+See the `GitHub contributor page <https://github.com/pymc-devs/pymc-extras/graphs/contributors>`_.
 
 .. toctree::
    :hidden:

docs/statespace/core.rst

@@ -2,7 +2,7 @@
 Statespace Core
 ********************
 
-.. automodule:: pymc_experimental.statespace.core
+.. automodule:: pymc_extras.statespace.core
 .. autosummary::
    :toctree: generated