Merge latest master & clean up release notes conflict

Author: michaelosthege

.github/workflows/dispatched_pre-commit.yml

@@ -0,0 +1,33 @@
+name: run pre-commit
+
+on:
+  repository_dispatch:
+    types: [pre-commit-run-command]
+jobs:
+  runPreCommit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          repository: ${{github.event.client_payload.pull_request.head.repo.full_name}}
+          ref: ${{github.event.client_payload.pull_request.head.ref}}
+          token: ${{ secrets.ACTION_TRIGGER_TOKEN }}
+      - name: Cache multiple paths
+        uses: actions/cache@v2
+        with:
+          path: |
+            ~/.cache/pre-commit
+            ~/.cache/pip
+          key: pre-commit-dispatched-${{ runner.os }}-build
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: install-pre-commit
+        run: python -m pip install --upgrade pre-commit
+      - name: Slash Command Dispatch
+        run: pre-commit run --all-files || (exit 0)
+      - run: |
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git commit -m "Run pre-commit" -a
+          git push

.github/workflows/pytest.yml

@@ -70,12 +70,12 @@ jobs:
       - name: Cache conda
         uses: actions/cache@v1
         env:
-          # Increase this value to reset cache if environment-dev-py36.yml has not changed
+          # Increase this value to reset cache if environment-dev-py39.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('conda-envs/environment-dev-py36.yml') }}
+            hashFiles('conda-envs/environment-dev-py39.yml') }}
       - name: Cache multiple paths
         uses: actions/cache@v2
         env:
@@ -90,18 +90,18 @@ jobs:
             hashFiles('requirements.txt') }}
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          activate-environment: pymc3-dev-py36
+          activate-environment: pymc3-dev-py39
           channel-priority: strict
-          environment-file: conda-envs/environment-dev-py36.yml
+          environment-file: conda-envs/environment-dev-py39.yml
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
       - name: Install-pymc3
         run: |
-          conda activate pymc3-dev-py36
+          conda activate pymc3-dev-py39
           pip install -e .
           python --version
       - name: Run tests
         run: |
-          conda activate pymc3-dev-py36
+          conda activate pymc3-dev-py39
           python -m pytest -vv --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1

.github/workflows/slash_dispatch.yml

@@ -0,0 +1,15 @@
+name: Slash Command Dispatch
+on:
+  issue_comment:
+    types: [created]
+jobs:
+  slashCommandDispatch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Slash Command Dispatch
+        uses: peter-evans/slash-command-dispatch@v2
+        with:
+          token: ${{ secrets.ACTION_TRIGGER_TOKEN }}
+          issue-type: pull-request
+          commands: |
+            pre-commit-run

.pre-commit-config.yaml

@@ -14,14 +14,15 @@ repos:
         exclude: ^requirements-dev\.txt$
     -   id: trailing-whitespace
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 0.5.4
+  rev: 0.5.5
   hooks:
     - id: nbqa-black
       additional_dependencies: [black==20.8b1]
     - id: nbqa-isort
       additional_dependencies: [isort==5.6.4]
     - id: nbqa-pyupgrade
       additional_dependencies: [pyupgrade==2.7.4]
+      args: [--py37-plus]
 - repo: https://github.com/PyCQA/isort
   rev: 5.6.4
   hooks:
@@ -31,7 +32,7 @@ repos:
   rev: v2.7.4
   hooks:
     - id: pyupgrade
-      args: [--py36-plus]
+      args: [--py37-plus]
 - repo: https://github.com/psf/black
   rev: 20.8b1
   hooks:

CONTRIBUTING.md

@@ -48,8 +48,8 @@ The preferred workflow for contributing to PyMC3 is to fork the [GitHub reposito
 4. Project requirements are in ``requirements.txt``, and libraries used for development are in ``requirements-dev.txt``. The easiest (and recommended) way to set up a development environment is via [miniconda](https://docs.conda.io/en/latest/miniconda.html):
 
    ```bash
-   $ conda env create -f conda-envs/environment-dev-py36.yml  # or py37 or py38
-   $ conda activate pymc3-dev-py36
+   $ conda env create -f conda-envs/environment-dev-py37.yml  # or py38 or py39
+   $ conda activate pymc3-dev-py37
    $ pip install -e .
    ```
 

README.rst

@@ -120,7 +120,7 @@ Dependencies
 ============
 
 PyMC3 is tested on Python 3.6, 3.7, and 3.8 and depends on `Theano-PyMC <https://github.com/pymc-devs/Theano-PyMC>`__,
-NumPy, SciPy, and Pandas
+NumPy, SciPy, and pandas
 (see `requirements.txt <https://github.com/pymc-devs/pymc3/blob/master/requirements.txt>`__ for version
 information).
 

RELEASE-NOTES.md

@@ -5,16 +5,22 @@ This release breaks some APIs w.r.t. `3.10.0`.
 It also brings some dreadfully awaited fixes, so be sure to go through the changes below.
 (Or latest when you run into problems.)
 
-### Maintenance
+### Breaking Changes
+- Python 3.6 support was dropped (by no longer testing) and Python 3.9 was added (see [#4332](https://github.com/pymc-devs/pymc3/pull/4332)).
 - Changed shape behavior: __No longer collapse length 1 vector shape into scalars.__ (see [#4206](https://github.com/pymc-devs/pymc3/issue/4206) and [#4214](https://github.com/pymc-devs/pymc3/pull/4214))
   - __Applies to random variables and also the `.random(size=...)` kwarg!__
   - To create scalar variables you must now use `shape=None` or `shape=()`.
   - __`shape=(1,)` and `shape=1` now become vectors.__ Previously they were collapsed into scalars
   - 0-length dimensions are now ruled illegal for random variables and raise a `ValueError`.
+- In `sample_prior_predictive` the `vars` kwarg was removed in favor of `var_names` (see [#4327](https://github.com/pymc-devs/pymc3/pull/4327)).
+- Removed `theanof.set_theano_config` because it illegally touched Theano's privates (see [#4329](https://github.com/pymc-devs/pymc3/pull/4329)).
+
+### New Features
+- ...
+
+### Maintenance
 - Fixed bug whereby partial traces returns after keyboard interrupt during parallel sampling had fewer draws than would've been available [#4318](https://github.com/pymc-devs/pymc3/pull/4318)
 - Make `sample_shape` same across all contexts in `draw_values` (see [#4305](https://github.com/pymc-devs/pymc3/pull/4305)).
-- Removed `theanof.set_theano_config` because it illegally touched Theano's privates (see [#4329](https://github.com/pymc-devs/pymc3/pull/4329)).
-- In `sample_prior_predictive` the `vars` kwarg was removed in favor of `var_names` (see [#4327](https://github.com/pymc-devs/pymc3/pull/4327))
 
 
 ## PyMC3 3.10.0 (7 December 2020)

conda-envs/environment-dev-py36.yml renamed to conda-envs/environment-dev-py39.yml

@@ -1,10 +1,8 @@
-name: pymc3-dev-py36
+name: pymc3-dev-py39
 channels:
 - conda-forge
 - defaults
 dependencies:
-- contextvars
-- dataclasses
 - h5py>=2.7
 - ipython>=7.16
 - libblas=*=*mkl
@@ -15,7 +13,7 @@ dependencies:
 - pytest-cov>=2.5
 - pytest>=3.0
 - python-graphviz
-- python=3.6
+- python=3.9
 - recommonmark>=0.4
 - sphinx-autobuild>=0.7
 - sphinx>=1.5

pymc3/backends/tracetab.py

@@ -26,7 +26,7 @@
 
 
 def trace_to_dataframe(trace, chains=None, varnames=None, include_transformed=False):
-    """Convert trace to Pandas DataFrame.
+    """Convert trace to pandas DataFrame.
 
     Parameters
     ----------

pymc3/data.py

@@ -462,7 +462,7 @@ class Data:
         A value to associate with this variable
     dims: {str, tuple of str}, optional, default=None
         Dimension names of the random variables (as opposed to the shapes of these
-        random variables). Use this when `value` is a Pandas Series or DataFrame. The
+        random variables). Use this when `value` is a pandas Series or DataFrame. The
         `dims` will then be the name of the Series / DataFrame's columns. See ArviZ
         documentation for more information about dimensions and coordinates:
         https://arviz-devs.github.io/arviz/notebooks/Introduction.html

pymc3/model.py

@@ -1682,7 +1682,7 @@ def init_value(self):
 
 
 def pandas_to_array(data):
-    """Convert a Pandas object to a NumPy array.
+    """Convert a pandas object to a NumPy array.
 
     XXX: When `data` is a generator, this will return a Theano tensor!
 

pyproject.toml

@@ -12,6 +12,3 @@ exclude_lines = [
 isort = 1
 black = 1
 pyupgrade = 1
-
-[tool.nbqa.addopts]
-pyupgrade = ["--py36-plus"]

requirements.txt

@@ -1,6 +1,4 @@
 arviz>=0.9.0
-contextvars; python_version < '3.7'
-dataclasses; python_version < '3.7'
 dill
 fastprogress>=0.2.0
 numpy>=1.13.0

setup.py

@@ -30,9 +30,9 @@
     "Development Status :: 5 - Production/Stable",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.6",
     "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
     "License :: OSI Approved :: Apache Software License",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering",
@@ -82,7 +82,7 @@ def get_version():
         # package_data={'docs': ['*']},
         include_package_data=True,
         classifiers=classifiers,
-        python_requires=">=3.6",
+        python_requires=">=3.7",
         install_requires=install_reqs,
         tests_require=test_reqs,
         test_suite="nose.collector",