Merge pull request #355 from BCG-Gamma/dev/2.1rc2

BUILD: release pytools 2.1rc2

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       - id: isort
 
@@ -11,7 +11,7 @@ repos:
         language: python_venv
         language_version: python39
 
-  - repo: https://gitlab.com/pycqa/flake8
+  - repo: https://github.com/pycqa/flake8
     rev: 5.0.4
     hooks:
       - id: flake8
@@ -34,11 +34,11 @@ repos:
         exclude: condabuild/meta.yaml
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.981
+    rev: v1.2.0
     hooks:
       - id: mypy
         files: src|sphinx|test
         language: python_venv
         language_version: python39
         additional_dependencies:
-          - numpy~=1.22
+          - numpy~=1.24

RELEASE_NOTES.rst

@@ -23,16 +23,43 @@ Release Notes
   correctly.
 
 
+*pytools* 2.1
+-------------
+
+2.1.0
+~~~~~
+
+- API: new decorator :obj:`.fitted_only` to mark methods that may only be
+  called after their associated object has been fitted using :meth:`.FittableMixin.fit`.
+- API: remove method ``ensure_fitted`` from :class:`.FittableMixin`, which is no longer
+  needed due to the new decorator :obj:`.fitted_only`.
+- API: new Sphinx callback :class:`.TrackCurrentClass` to keep track of the current
+  class being processed by *autodoc*.
+- API: new Sphinx callback :class:`.RenamePrivateArguments` to rename private
+  “positional-only” arguments in a function's signature (with two leading underscores)
+  back to their original names in the source code, so that *autodoc* can pick them up
+  correctly.
+- API: :class:`.Expression` objects support plain text and HTML output in Jupyter
+  notebooks
+
+
 *pytools* 2.0
 -------------
 
-*pytools* 2.0 features enhanced visualisations together with additional API improvements,
+*pytools* 2 introduces enhanced visualisations along with additional API improvements,
 and is now subject to static type checking with |mypy|.
 
+
+2.0.6
+~~~~~
+
+- BUILD: add support for :mod:`pandas` |nbsp| 2.0 and above
+
+
 2.0.5
 ~~~~~
 
-- API: de-dent docstrings before processing them with the :obj:``.subsdoc`` decorator
+- API: de-dent docstrings before processing them with the :obj:`.subsdoc` decorator
 - FIX: in method :meth:`.AllTracker.resolve_forward_references`, unwrap functions before
   accessing their ``__globals__`` attribute
 

azure-pipelines.yml

@@ -54,7 +54,7 @@ stages:
               versionSpec: '3.9'
             displayName: 'use Python 3.9'
           - script: |
-              python -m pip install isort~=5.10
+              python -m pip install isort~=5.12
               python -m isort --check --diff .
             displayName: 'Run isort'
       - job:
@@ -87,7 +87,7 @@ stages:
               versionSpec: '3.9'
             displayName: 'use Python 3.9'
           - script: |
-              python -m pip install mypy~=0.981 numpy~=1.22
+              python -m pip install mypy~=1.2.0 numpy~=1.24
               python -m mypy src
             displayName: 'Run mypy'
 
@@ -101,17 +101,20 @@ stages:
         displayName: 'detect changes'
         steps:
           - checkout: self
+            fetchDepth: 2
 
           - task: Bash@3
             name: diff
             inputs:
               targetType: 'inline'
               script: |
+                set -eux
+
                 echo Repo: $(Build.DefinitionName)
                 cd $(System.DefaultWorkingDirectory)
-                files_changed=$(git diff $(Build.SourceVersion)^! --name-only)
+                files_changed=$(git diff $(Build.SourceVersion)^ --name-only)
                 echo "Files changed since last commit: ${files_changed}"
-                n_files_changed=$(git diff $(Build.SourceVersion)^! --name-only | grep -i -E 'meta\.yaml|pyproject\.toml|azure-pipelines\.yml|tox\.ini|make\.py'  | wc -l | xargs)
+                n_files_changed=$(git diff $(Build.SourceVersion)^ --name-only | grep -i -E 'meta\.yaml|pyproject\.toml|azure-pipelines\.yml|tox\.ini|make\.py'  | wc -l | xargs)
                 if [ ${n_files_changed} -gt 0 ]
                 then
                 build_changed=1
@@ -141,8 +144,8 @@ stages:
         steps:
           - task: UsePythonVersion@0
             inputs:
-              versionSpec: '3.8'
-            displayName: 'use Python 3.8'
+              versionSpec: '3.9'
+            displayName: 'use Python 3.9'
 
           - checkout: self
 
@@ -153,10 +156,15 @@ stages:
               targetType: 'inline'
               script: |
                 set -eux
-                eval "$(conda shell.bash hook)"
 
-                conda env create
-                conda activate $(project_name)-develop
+                # install micromamba
+                curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+                export MAMBA_ROOT_PREFIX=~/micromamba
+                eval "$(./bin/micromamba shell hook -s posix)"
+
+                # install the develop environment
+                micromamba env create --yes --file environment.yml
+                micromamba activate $(project_name)-develop
 
                 export PYTHONPATH=$(System.DefaultWorkingDirectory)/src/
                 export RUN_PACKAGE_VERSION_TEST=$(project_name)
@@ -409,8 +417,8 @@ stages:
         steps:
           - task: UsePythonVersion@0
             inputs:
-              versionSpec: '3.8'
-            displayName: 'use Python 3.8'
+              versionSpec: '3.9'
+            displayName: 'use Python 3.9'
 
           - checkout: pytools
           - checkout: self
@@ -474,8 +482,8 @@ stages:
         steps:
           - task: UsePythonVersion@0
             inputs:
-              versionSpec: '3.8'
-            displayName: 'use Python 3.8'
+              versionSpec: '3.9'
+            displayName: 'use Python 3.9'
 
           - checkout: pytools
           - checkout: self
@@ -601,8 +609,8 @@ stages:
         steps:
           - task: UsePythonVersion@0
             inputs:
-              versionSpec: '3.8'
-            displayName: 'use Python 3.8'
+              versionSpec: '3.9'
+            displayName: 'use Python 3.9'
 
           - task: InstallSSHKey@0
             inputs:
@@ -611,7 +619,6 @@ stages:
               sshKeySecureFile: 'deploy_docs_$(project_name)'
             displayName: 'Install the deploy SSH key'
 
-          - checkout: pytools
           - checkout: self
 
           - script: dir $(Build.SourcesDirectory)
@@ -622,7 +629,7 @@ stages:
               script: |
                 set -eux
 
-                cd $(System.DefaultWorkingDirectory)/$(project_root)
+                cd $(System.DefaultWorkingDirectory)
                 echo "Checking out github-pages"
                 git checkout --track origin/github-pages
 
@@ -642,16 +649,20 @@ stages:
               targetType: 'inline'
               script: |
                 set -eux
-                eval "$(conda shell.bash hook)"
 
-                cd $(System.DefaultWorkingDirectory)/$(project_root)
+                cd $(System.DefaultWorkingDirectory)
                 echo "Checking out $(branchName)"
                 git checkout $(branchName)
 
-                conda env create
-                conda activate $(project_name)-develop
+                # install micromamba
+                curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+                export MAMBA_ROOT_PREFIX=~/micromamba
+                eval "$(./bin/micromamba shell hook -s posix)"
+                # install the develop environment
+                micromamba env create --yes --file environment.yml
+                micromamba activate $(project_name)-develop
 
-                export PYTHONPATH=$(System.DefaultWorkingDirectory)/$(project_root)/src/
+                export PYTHONPATH=$(System.DefaultWorkingDirectory)/src/
 
                 python sphinx/make.py html
 
@@ -662,21 +673,22 @@ stages:
               targetType: 'inline'
               script: |
                 set -eux
-                eval "$(conda shell.bash hook)"
+                export MAMBA_ROOT_PREFIX=~/micromamba
+                eval "$(./bin/micromamba shell hook -s posix)"
 
                 # install the tree utility
                 sudo apt-get install tree
 
-                cd $(System.DefaultWorkingDirectory)/$(project_root)
+                cd $(System.DefaultWorkingDirectory)
 
                 echo "Restoring previous documentation to the docs directory"
                 mkdir -p docs
                 mv $(Build.ArtifactStagingDirectory)/docs-version.bak docs/docs-version
                 ls docs/docs-version
 
-                mkdir -p $(System.DefaultWorkingDirectory)/$(project_root)/sphinx/build/
+                mkdir -p $(System.DefaultWorkingDirectory)/sphinx/build/
 
-                conda activate $(project_name)-develop
+                micromamba activate $(project_name)-develop
                 python sphinx/make.py prepare_docs_deployment
 
                 echo "Current docs contents:"
@@ -708,7 +720,7 @@ stages:
               targetType: 'inline'
               script: |
                 set -eux
-                cd $(System.DefaultWorkingDirectory)/$(project_root)
+                cd $(System.DefaultWorkingDirectory)
 
                 echo "Adjusting git credentials"
                 git config --global user.name "Azure Pipelines"

environment.yml

@@ -4,36 +4,36 @@ channels:
   - bcg_gamma
 dependencies:
   # run
-  - joblib ~= 1.1
-  - matplotlib ~= 3.5
-  - numpy ~= 1.22
-  - pandas ~= 1.4
+  - joblib ~= 1.2
+  - matplotlib ~= 3.6
+  - numpy ~= 1.23
+  - pandas ~= 2.0
   - python ~= 3.9
-  - scipy ~= 1.8
+  - scipy ~= 1.10
   - typing_extensions ~= 4.3
   - typing_inspect ~= 0.7
   # build/test
-  - conda-build ~= 3.21
-  - conda-verify ~= 3.1
-  - docutils ~= 0.17
-  - flit ~= 3.0
-  - jinja2 ~= 2.11
+  - conda-build ~= 3.23.3
+  - conda-verify ~= 3.1.1
+  - docutils ~= 0.17.1
+  - flit ~= 3.8.0
+  - jinja2 ~= 2.11.3
   - markupsafe ~= 2.0.1  # markupsafe 2.1 breaks support for jinja2
-  - m2r ~= 0.2
-  - pluggy ~= 0.13
-  - pre-commit ~= 2.20
-  - pytest ~= 7.1
-  - pytest-cov ~= 2.12
-  - pyyaml ~= 5.4
-  - toml ~= 0.10
-  - tox ~= 3.24
-  - yaml ~= 0.2
+  - m2r ~= 0.3.1
+  - pluggy ~= 0.13.1
+  - pre-commit ~= 2.21.0
+  - pytest ~= 7.2.1
+  - pytest-cov ~= 2.12.1
+  - pyyaml ~= 5.4.1
+  - toml ~= 0.10.2
+  - tox ~= 3.27.1
+  - yaml ~= 0.2.5
   # sphinx
-  - sphinx ~= 4.5
-  - sphinx-autodoc-typehints ~= 1.19
   - nbsphinx ~= 0.8.9
+  - sphinx ~= 4.5.0
+  - sphinx-autodoc-typehints ~= 1.19.2
   - pydata-sphinx-theme ~= 0.8.1
   # notebooks
-  - jupyterlab ~= 3.2
-  - openpyxl ~= 3.0
-  - seaborn ~= 0.11
+  - jupyterlab ~= 3.5.2
+  - openpyxl ~= 3.0.10
+  - seaborn ~= 0.12.2

pyproject.toml

@@ -16,8 +16,8 @@ license = "Apache Software License v2.0"
 requires = [
     "joblib            >=0.14,<2a",
     "matplotlib        ~=3.0",
-    "numpy             >=1.21,<2a",
-    "pandas            >=0.24,<2a",
+    "numpy             >=1.21,<2a",  # cannot use ~= due to conda bug
+    "pandas            >=1",
     "scipy             ~=1.2",
     "typing_inspect    ~=0.4",
     "typing_extensions ~=4.0",
@@ -44,10 +44,7 @@ classifiers = [
 [tool.flit.metadata.requires-extra]
 testing = [
     "pytest ~= 7.1",
-    "pytest-cov ~= 2.8",
-    "flake8 ~= 3.8",
-    "flake8-comprehensions ~= 3.2",
-    "isort ~= 5.5",
+    "pytest-cov ~= 2.12",
 ]
 docs = [
     "sphinx ~= 4.5",
@@ -74,8 +71,8 @@ no-binary.min = ["matplotlib"]
 joblib            = "~=0.14.0"
 matplotlib        = "~=3.0.3"
 numpy             = "==1.21.6"  # cannot use ~= due to conda bug
-pandas            = "~=0.24.2"
-python            = "==3.7.12"  # cannot use ~= due to conda bug
+pandas            = "~=1.0.5"
+python            = ">=3.7.12,<3.8a"    # cannot use ~= due to conda bug
 scipy             = "~=1.2.1"
 typing_inspect    = "~=0.4.0"
 typing_extensions = "~=4.0.0"
@@ -84,8 +81,8 @@ typing_extensions = "~=4.0.0"
 # maximum requirements of gamma-pytools
 joblib            = "~=1.1"
 matplotlib        = "~=3.5"
-numpy             = ">=1.23,<2a"  # cannot use ~= due to conda bug
-pandas            = "~=1.4"
+numpy             = ">=1.24,<2a"  # cannot use ~= due to conda bug
+pandas            = "~=2.0"
 python            = ">=3.9,<4a"   # cannot use ~= due to conda bug
 scipy             = "~=1.8"
 typing_inspect    = "~=0.7"

src/pytools/__init__.py

@@ -1,4 +1,4 @@
 """
 A collection of Python extensions and tools used in BCG GAMMA's open-source libraries.
 """
-__version__ = "2.1rc1"
+__version__ = "2.1rc2"

src/pytools/data/_matrix.py

@@ -128,7 +128,7 @@ def _arg_to_array(
             if axis_arg is None:
                 return None
             else:
-                arr = np.array(axis_arg)
+                arr = np.asarray(axis_arg)
                 if arr.ndim != 1:
                     raise ValueError(
                         f"arg {arg_name_}[{axis}] must be a 1d array, but has "