Merge from develop (#203)

* ci: mypy dependency * ci: update dependencies * ci: update dependencies * prevent numpy warnings (#184) * refactor: numpy complex * refactor: numpy float * refactor: numpy bool * refactor: numpy float64 * ci: update dependencies * ci: setup Github Actions * ci: exclude spark from tests * ci: disable pytest-spark * ci: remove travis * updated readme (#188) * ci: pre-commit updates * test: fix error in tests * ci: update dependencies * spark requirement + complex fix (#186) test: fixes to bring tests up to date * spark requirement + complex fix * updated numpy object implementation * old reference to bottleneck * a regression in old numpy * fix: email address and URL python backend resolves three bugs in the two types in the Python backend: - EmailAddress had two relationships registered rather than a relationship and and a transformer - URL contains_op had a typo - URL relationship wasn't correctly checking for scheme and netloc. * ci: upgrading packages * WIP: Tests/python backend (#189) * spark requirement + complex fix * updated numpy object implementation * old reference to bottleneck * fixes complex tests and a regression in old numpy * isort * wip-setup * removed pandas references in python tests; * spark requirement + complex fix * updated numpy object implementation * old reference to bottleneck * fixes complex tests and a regression in old numpy * isort * wip-setup * removed pandas references in python tests; * Update version.py * ci: update dependencies * ci: upgrading packages * ci: pre-commit updates * fix : import ABCIndex in place of ABCIndexClass * fix : import ABCIndex in place of ABCIndexClass Pandas 1.3 renamed the ABCIndexClass to ABCIndex, so this should make the trick. Backwards compatible. Co-authored-by: Simon Brugman <[email protected]> * Update version.py * ci: dependency update * ci: update dependencies * ci: update dependencies * ci: dependency update * ci: upgrading packages * ci: pre-commit updates * ci: pre-commit updates * Readme Updates (#193) * using section * readme rewrite * language updates * test * manifest * increased logo size * typo * backend notes * ci: update dependencies * ci: update dependencies * ci: dependency update * ci: update dependencies * ci: pre-commit updates * ci: upgrading packages * ci: upgrading packages * ci: update dependencies * ci: dependency update * ci: update dependencies * ci: python 3.6 end of life * fix typo (#195) * ci: dependency update * ci: update dependencies * ci: update dependencies * ci: upgrading packages * ci: update dependencies * ci: update dependencies * ci: upgrading packages * ci: pre-commit updates * ci: upgrading packages * ci: dependency update * ci: update dependencies * ci: upgrading packages * ci: dependency update * ci: upgrading packages * Remove tangled_up_in_unicode dep (#197) It's not required since May 2021 (4ce2507) Refs dylan-profiler/tangled-up-in-unicode#10 * ci: pre-commit updates * ci: dependency update * ci: pre-commit updates * fixed numpy and numba deprecations * 0.7.6 (#202) * bump * old * 3.10 * lint * lint * removed 3.8 from tests * remove mypy from precommit * flake8 complaint * black * test updates * "lint * numpy differences * lint * integer->float * integer->float * pandas numpy roundtripping variation * lint --------- Co-authored-by: Simon Brugman <[email protected]> Co-authored-by: Charles-Meldhine Madi Mnemoi <[email protected]> Co-authored-by: Gustavo Camargo <[email protected]> Co-authored-by: Aarni Koskela <[email protected]>
dylan-profiler · Feb 6, 2024 · 076affa · 076affa
1 parent dca86aa
commit 076affa
Show file tree

Hide file tree

Showing 40 changed files with 497 additions and 206 deletions.
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
@@ -2,47 +2,47 @@ name: Deploy to PyPi
 
 on:
   release:
-      types: [created]
-  
+    types: [ created ]
+
 jobs:
   release:
     if: github.event_name == 'release' && github.event.action == 'created'
     name: PyPi Release
     runs-on: ubuntu-latest
-
+    
     steps:
     - uses: actions/checkout@v2
       name: Checkout repo
-
-    - name: Set up Python 3.8
+    
+    - name: Set up Python 3.12
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
-
+        python-version: 3.12
+    
     - uses: actions/cache@v1
       name: Cache pip dependencies
       with:
         path: ~/.cache/pip
         key: ${{ runner.os }}-pip-${{ hashFiles('requirements*.txt') }}
         restore-keys: |
           ${{ runner.os }}-pip-
-
+    
     - name: Install pip dependencies
       run: |
-         pip install --upgrade pip
-         pip install -r requirements.txt
-         pip install -r requirements_dev.txt
-         pip install -r requirements_test.txt
-
+        pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -r requirements_dev.txt
+        pip install -r requirements_test.txt
+    
     - name: Install
       run: make install
-
+    
     - name: Make distribution
       run: |
         check-manifest
         python setup.py sdist bdist_wheel
         twine check dist/*
-
+    
     - name: Publish a Python distribution to PyPI
       uses: pypa/gh-action-pypi-publish@master
       with:

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -10,10 +10,10 @@ jobs:
   test:
     strategy:
       matrix:
-        os: [ubuntu-latest]
-        python: [3.6, 3.7, 3.8]
+        os: [ ubuntu-latest ]
+        python: [ 3.8, 3.9, "3.10", 3.11, 3.12 ]
     runs-on: ${{ matrix.os }}
-
+    
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python }}

diff --git a/.gitignore b/.gitignore
@@ -6,6 +6,7 @@ docsrc/source/visions/api/_autosummary/
 docsrc/build/
 plots/*/
 playground/
+.vscode/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,22 +1,22 @@
 repos:
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.29.1
+    rev: v3.15.0
     hooks:
     -   id: pyupgrade
         args: ['--py36-plus','--exit-zero-even-if-changed']
 -   repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+
+    rev: 5.13.2
     hooks:
       - id: isort
-        files: '.*'
-        args: ['--profile=black']
+        args: ["--profile", "black", "--filter-files"]
 -   repo: https://github.com/psf/black
-    rev: 21.11b1
+    rev: 24.1.1
     hooks:
     - id: black
       language_version: python
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+-   repo: https://github.com/PyCQA/flake8
+    rev: 7.0.0
     hooks:
     - id: flake8
       # TODO: remove F40x, E772 and fix errors
@@ -26,17 +26,17 @@ repos:
         # - flake8-print
         - flake8-2020
 -   repo: https://github.com/mgedmin/check-manifest
-    rev: "0.47"
+    rev: "0.49"
     hooks:
     -   id: check-manifest
--   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v0.910-1'
-    hooks:
-    -   id: mypy
-        files: '^src/'
-        additional_dependencies:
-          - types-attrs
+# -   repo: https://github.com/pre-commit/mirrors-mypy
+#     rev: 'v1.8.0'
+#     hooks:
+#     -   id: mypy
+#         files: '^src/'
+#         additional_dependencies:
+#           - types-attrs
 -   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
     -   id: rst-backticks
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,10 +1,10 @@
 include LICENSE
 include README.md
-include SIDNfonds.png
 include requirements*.txt
 include src/visions/py.typed
 include *.yaml
 recursive-include src *.md
+recursive-include images *.png
 
 exclude Makefile make.bat
 recursive-include src *.py
@@ -24,11 +24,12 @@ exclude src/visions/visualisation/summaries src/visions/visualisation/typesets
 recursive-exclude src/visions/visualisation/summaries *
 recursive-exclude src/visions/visualisation/typesets *
 
+
 # Include template
 include src/visions/visualisation/circular_packing.html
 
 # Exclude directories
 exclude docs docsrc paper
 recursive-exclude docs *
 recursive-exclude docsrc *
-recursive-exclude paper *
+recursive-exclude paper *