Deprecate those kwargs in v3 that will break in v4 (#5226)

* Upgrade pre-commit from main and apply automated code style

Except the check against print statements.

* XFAIL KroneckerNormal test on Windows because of #5253

* Add deprecat dependency

For more automation in kwarg deprecations.

* Deprecation of testval→initval and related start kwarg

* Partially add admonition style for rendering warnings

With css taken from pydata-sphinx-theme.

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

Author: michaelosthege

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ^(docs/logos|pymc3/tests/data)/
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.4.0
+  rev: v4.0.1
   hooks:
     -   id: check-merge-conflict
     -   id: check-toml
@@ -14,44 +14,43 @@ repos:
         exclude: ^requirements-dev\.txt$
     -   id: trailing-whitespace
 - repo: https://github.com/PyCQA/isort
-  rev: 5.7.0
+  rev: 5.10.1
   hooks:
     - id: isort
       name: isort
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.10.0
+  rev: v2.29.1
   hooks:
     - id: pyupgrade
       args: [--py37-plus]
 - repo: https://github.com/psf/black
-  rev: 20.8b1
+  rev: 21.12b0
   hooks:
     - id: black
 - repo: https://github.com/PyCQA/pylint
-  rev: pylint-2.6.0
+  rev: v2.12.2
   hooks:
     - id: pylint
       args: [--rcfile=.pylintrc]
-      files: ^pymc3/
+      files: ^pymc/
+- repo: https://github.com/MarcoGorelli/madforhooks
+  rev: 0.2.1
+  hooks:
+    - id: conda-env-sorter
+      files: ^conda-envs/environment-dev-py.+\.yml$
 - repo: local
   hooks:
     - id: check-no-tests-are-ignored
+      additional_dependencies: [pandas,pyyaml]
       entry: python scripts/check_all_tests_are_covered.py
       files: ^\.github/workflows/pytest\.yml$
       language: python
       name: Check no tests are ignored
       pass_filenames: false
-    - id: conda-env-sort
-      additional_dependencies: [pyyaml]
-      entry: python scripts/sort_conda_envs.py
-      files: ^conda-envs/environment-dev-py37\.yml$
-      language: python
-      name: Sort dependencies in conda envs
-      types: [yaml]
     - 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

RELEASE-NOTES.md

@@ -3,6 +3,8 @@
 ## PyMC 3.11.5 (TBD)
 ### Backports
 + The `pm.logp(rv, x)` syntax is now available and recommended to make your model code `v4`-ready. Note that this backport is just an alias and much less capable than what's available with `pymc >=4` (see [#5083](https://github.com/pymc-devs/pymc/pulls/5083)).
++ The `pm.Distribution(testval=...)` kwarg was deprecated and will be replaced by `pm.Distribution(initval=...)`in `pymc >=4` (see [#5226](https://github.com/pymc-devs/pymc/pulls/5226)).
++ The `pm.sample(start=...)` kwarg was deprecated and will be replaced by `pm.sample(initvals=...)`in `pymc >=4` (see [#5226](https://github.com/pymc-devs/pymc/pulls/5226)).
 
 ## PyMC3 3.11.4 (20 August 2021)
 

conda-envs/environment-dev-py37.yml

@@ -11,6 +11,7 @@ dependencies:
 - numpy=1.15
 - numpydoc>=0.9
 - pandas=0.24
+- pip
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
@@ -21,3 +22,5 @@ dependencies:
 - sphinx-autobuild>=0.7
 - sphinx>=1.5
 - watermark
+- pip:
+  - deprecat

conda-envs/environment-dev-py38.yml

@@ -9,6 +9,7 @@ dependencies:
 - mkl-service
 - nbsphinx>=0.4
 - numpydoc>=0.9
+- pip
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
@@ -18,3 +19,5 @@ dependencies:
 - sphinx-autobuild>=0.7
 - sphinx>=1.5
 - watermark
+- pip:
+  - deprecat

conda-envs/environment-dev-py39.yml

@@ -9,6 +9,7 @@ dependencies:
 - mkl-service
 - nbsphinx>=0.4
 - numpydoc>=0.9
+- pip
 - pre-commit>=2.8.0
 - pytest-cov>=2.5
 - pytest>=3.0
@@ -18,3 +19,5 @@ dependencies:
 - sphinx-autobuild>=0.7
 - sphinx>=1.5
 - watermark
+- pip:
+  - deprecat

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

@@ -24,3 +24,5 @@ dependencies:
 - sphinx-autobuild>=0.7
 - sphinx>=1.5
 - watermark
+- pip:
+  - deprecat

docs/source/_static/main.css

@@ -3,3 +3,130 @@
     margin: 0.5em;
     content: ":";
 }
+
+:root {
+  --pst-color-primary: 19, 6, 84;
+  --pst-color-success: 40, 167, 69;
+  --pst-color-info: 0, 123, 255; /*23, 162, 184;*/
+  --pst-color-warning: 255, 193, 7;
+  --pst-color-danger: 220, 53, 69;
+  --pst-color-text-base: 51, 51, 51;
+
+  --pst-color-admonition-default: var(--pst-color-info);
+  --pst-color-admonition-note: var(--pst-color-info);
+  --pst-color-admonition-attention: var(--pst-color-warning);
+  --pst-color-admonition-caution: var(--pst-color-warning);
+  --pst-color-admonition-warning: var(--pst-color-warning);
+  --pst-color-admonition-danger: var(--pst-color-danger);
+  --pst-color-admonition-error: var(--pst-color-danger);
+  --pst-color-admonition-hint: var(--pst-color-success);
+  --pst-color-admonition-tip: var(--pst-color-success);
+  --pst-color-admonition-important: var(--pst-color-success);
+}
+
+.admonition,
+div.admonition {
+ margin:1.5625em auto;
+ padding:0 .6rem .8rem;
+ overflow:hidden;
+ page-break-inside:avoid;
+ border-left:.2rem solid;
+ border-left-color:rgba(var(--pst-color-admonition-default),1);
+ border-bottom-color:rgba(var(--pst-color-admonition-default),1);
+ border-right-color:rgba(var(--pst-color-admonition-default),1);
+ border-top-color:rgba(var(--pst-color-admonition-default),1);
+ border-radius:.2rem;
+ box-shadow:0 .2rem .5rem rgba(0,0,0,.05),0 0 .0625rem rgba(0,0,0,.1);
+ transition:color .25s,background-color .25s,border-color .25s
+}
+.admonition :last-child,
+div.admonition :last-child {
+ margin-bottom:0
+}
+.admonition p.admonition-title~*,
+div.admonition p.admonition-title~* {
+ padding:0 1.4rem
+}
+.admonition>ol,
+.admonition>ul,
+div.admonition>ol,
+div.admonition>ul {
+ margin-left:1em
+}
+.admonition>.admonition-title,
+div.admonition>.admonition-title {
+ position:relative;
+ margin:0 -.6rem;
+ padding:.4rem .6rem .4rem 2rem;
+ font-weight:700;
+ background-color:rgba(var(--pst-color-admonition-default),.1)
+}
+.admonition>.admonition-title+*,
+div.admonition>.admonition-title+* {
+ margin-top:.4em
+}
+.admonition.attention,
+div.admonition.attention {
+ border-color:rgba(var(--pst-color-admonition-attention),1)
+}
+.admonition.attention>.admonition-title,
+div.admonition.attention>.admonition-title {
+ background-color:rgba(var(--pst-color-admonition-attention),.1)
+}
+.admonition.caution,
+div.admonition.caution {
+ border-color:rgba(var(--pst-color-admonition-caution),1)
+}
+.admonition.caution>.admonition-title,
+div.admonition.caution>.admonition-title {
+ background-color:rgba(var(--pst-color-admonition-caution),.1)
+}
+div.admonition.warning {
+ border-color:rgba(var(--pst-color-admonition-warning),1)
+}
+.admonition.warning>.admonition-title,
+div.admonition.warning>.admonition-title {
+ background-color:rgba(var(--pst-color-admonition-warning),.1)
+}
+div.admonition.danger {
+ border-color:rgba(var(--pst-color-admonition-danger),1)
+}
+.admonition.danger>.admonition-title,
+div.admonition.danger>.admonition-title {
+ background-color:rgba(var(--pst-color-admonition-danger),.1)
+}
+div.admonition.error {
+ border-color:rgba(var(--pst-color-admonition-error),1)
+}
+.admonition.error>.admonition-title,
+div.admonition.error>.admonition-title {
+ background-color:rgba(var(--pst-color-admonition-error),.1)
+}
+div.admonition.hint {
+ border-color:rgba(var(--pst-color-admonition-hint),1)
+}
+.admonition.hint>.admonition-title,
+div.admonition.hint>.admonition-title {
+ background-color:rgba(var(--pst-color-admonition-hint),.1)
+}
+div.admonition.tip {
+ border-color:rgba(var(--pst-color-admonition-tip),1)
+}
+.admonition.tip>.admonition-title,
+div.admonition.tip>.admonition-title {
+ background-color:rgba(var(--pst-color-admonition-tip),.1)
+}
+div.admonition.important {
+ border-color:rgba(var(--pst-color-admonition-important),1)
+}
+.admonition.important>.admonition-title,
+div.admonition.important>.admonition-title {
+ background-color:rgba(var(--pst-color-admonition-important),.1)
+}
+div.admonition.note {
+ border-color:rgba(var(--pst-color-admonition-note),1)
+}
+.admonition.note>.admonition-title,
+div.admonition.note>.admonition-title {
+ background-color:rgba(var(--pst-color-admonition-note),.1)
+}

docs/source/sphinxext/gallery_generator.py

@@ -194,7 +194,7 @@ def build_gallery(srcdir, gallery):
     with open(table_of_contents_file) as toc:
         table_of_contents = toc.read()
 
-    js_contents = "Gallery.examples = {}\n{}".format(json.dumps(data), table_of_contents)
+    js_contents = f"Gallery.examples = {json.dumps(data)}\n{table_of_contents}"
 
     with open(js_file, "w") as js:
         js.write(js_contents)

pymc3/__init__.py

@@ -63,7 +63,7 @@ def __set_compiler_flags():
 
 
 def _hotfix_theano_printing():
-    """ This is a workaround for https://github.com/pymc-devs/aesara/issues/309 """
+    """This is a workaround for https://github.com/pymc-devs/aesara/issues/309"""
     try:
         import pydot
         import theano.printing

pymc3/backends/base.py

@@ -364,7 +364,7 @@ def __getattr__(self, name):
             return self.get_values(name)
         if name in self.stat_names:
             return self.get_sampler_stats(name)
-        raise AttributeError("'{}' object has no attribute '{}'".format(type(self).__name__, name))
+        raise AttributeError(f"'{type(self).__name__}' object has no attribute '{name}'")
 
     def __len__(self):
         chain = self.chains[-1]