Merge paper version to main

.github/workflows/checks.yml

@@ -12,7 +12,7 @@ jobs:
       - name: set up python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.10.4'
 
       - name: set PY
         run: echo "PY=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV

.github/workflows/tests.yml

@@ -5,16 +5,14 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: '3.8'
-    - name:
-        Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install pytest
-    - name: Test with pytest
-      run: |
-        pip install -e .
-        pytest
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10.4'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+      - name: Test with pytest
+        run: |
+          python -m pip install -e ".[test]"
+          python -m pytest -s -W ignore

.gitignore

@@ -130,3 +130,13 @@ dmypy.json
 
 # not change default config
 configs/avae-test-config.yml
+
+# remove mac specific files
+.DS_Store
+
+# remove pycharm specific files
+.idea/
+affinity-vae.code-workspace
+.vscode/launch.json
+.vscode/settings.json
+.gitignore

.pre-commit-config.yaml

@@ -1,28 +1,52 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
 repos:
-    - repo: https://github.com/pycqa/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.2.0
-      hooks:
-          - id: check-docstring-first
-          - id: check-executables-have-shebangs
-          - id: check-merge-conflict
-          - id: check-toml
-          - id: end-of-file-fixer
-          - id: mixed-line-ending
-            args: [--fix=lf]
-          - id: requirements-txt-fixer
-          - id: trailing-whitespace
-            args: [--markdown-linebreak-ext=md]
-    - repo: https://github.com/PyCQA/flake8
-      rev: 6.0.0
-      hooks:
-          - id: flake8
-            # this seems to need to be here in addition to setup.cfg
-            exclude: __init__.py|examples
-    - repo: https://github.com/psf/black
-      rev: 22.3.0
-      hooks:
-          - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.4.0"
+    hooks:
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+    #- repo: https://github.com/pre-commit/mirrors-prettier
+    #rev: "v3.0.3"
+    #    hooks:
+    #  - id: prettier
+    #    types_or: [yaml, markdown, html, css, scss, javascript, json]
+    #    args: [--prose-wrap=always]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.7.1'  # Use the sha / tag you want to point at
+    hooks:
+      -  id: mypy
+         language_version: python3.10
+         args: [--ignore-missing-imports]
+         additional_dependencies: ['types-PyYAML']

LICENSE.md

@@ -1,10 +1,9 @@
 BSD 3-Clause License
 
-Copyright (c) 2022, Alan Turing Institute
-All rights reserved.
+Copyright (c) 2022, Alan Turing Institute All rights reserved.
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
 
 1. Redistributions of source code must retain the above copyright notice, this
    list of conditions and the following disclaimer.
@@ -13,17 +12,17 @@ modification, are permitted provided that the following conditions are met:
    this list of conditions and the following disclaimer in the documentation
    and/or other materials provided with the distribution.
 
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software without
+   specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.