reflectorch 1.4.0__tar.gz → 1.5.0__tar.gz

{reflectorch-1.4.0 → reflectorch-1.5.0}/.dockerignore

@@ -1,3 +1,3 @@
-saved_models/
-saved_losses/
+saved_models/
+saved_losses/
 triton_models/

{reflectorch-1.4.0 → reflectorch-1.5.0}/.github/workflows/ci.yml

@@ -1,40 +1,40 @@
-name: CI
-
-on:
-  push:
-    branches:
-      - master
-  pull_request:
-    branches:
-      - master
-
-jobs:
-  build:
-    name: Build Run (${{ matrix.python-version }}, ${{ matrix.os }})
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install package (with build and tests dependencies)
-      run: python -m pip install .[build,tests,docs]
-
-    - name: Run tests
-      run: pytest tests/ --cov=reflectorch --cov-report=xml
-
-    - name: Use Codecov to track coverage
-      uses: codecov/codecov-action@v2
-      with:
-        files: ./coverage.xml
-
-    - name: Build distribution
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build:
+    name: Build Run (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install package (with build and tests dependencies)
+      run: python -m pip install .[build,tests,docs]
+
+    - name: Run tests
+      run: pytest tests/ --cov=reflectorch --cov-report=xml
+
+    - name: Use Codecov to track coverage
+      uses: codecov/codecov-action@v2
+      with:
+        files: ./coverage.xml
+
+    - name: Build distribution
       run: python -m build

{reflectorch-1.4.0 → reflectorch-1.5.0}/.github/workflows/draft-pdf.yml

@@ -1,24 +1,24 @@
-name: Draft PDF
-on: [push]
-
-jobs:
-  paper:
-    runs-on: ubuntu-latest
-    name: Paper Draft
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Build draft PDF
-        uses: openjournals/openjournals-draft-action@master
-        with:
-          journal: joss
-          # This should be the path to the paper within your repo.
-          paper-path: paper/paper.md
-      - name: Upload
-        uses: actions/upload-artifact@v4
-        with:
-          name: paper
-          # This is the output path where Pandoc will write the compiled
-          # PDF. Note, this should be the same directory as the input
-          # paper.md
+name: Draft PDF
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
           path: paper/paper.pdf

reflectorch-1.5.0/.github/workflows/publish.yml

@@ -0,0 +1,42 @@
+name: Publish to PyPI (Trusted Publishing)
+
+on:
+  push:
+    tags:
+      - "v*"            # run when you push a tag like v1.2.3
+  workflow_dispatch:    # allow manual runs (from the actions tab)
+
+jobs:
+  build-dist:
+    name: Build sdist + wheel
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: python -m pip install --upgrade pip build
+      - run: python -m build
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  pypi-publish:
+    name: Upload release to PyPI
+    needs: build-dist
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

{reflectorch-1.4.0 → reflectorch-1.5.0}/.gitignore

@@ -1,44 +1,46 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-*.so
-*.sh
-*.exe
-#*.ipynb
-
-*.pt
-*.h5
-*.safetensors
-
-# Distribution / packaging
-.Python
-venv
-.venv
-.vscode
-.idea
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-#Documentation
-documentation/_build/*
-
-# Don't ignore .pt files in the exp_data directory
-!exp_data/*.pt
-
-#Other
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+*.so
+*.sh
+*.exe
+#*.ipynb
+.ipynb_checkpoints/
+
+*.pt
+*.h5
+*.safetensors
+
+# Distribution / packaging
+.Python
+venv
+.venv
+.vscode
+.idea
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+figures/
+
+#Documentation
+documentation/_build/*
+
+# Don't ignore .pt files in the exp_data directory
+!exp_data/*.pt
+
+#Other
 tensorboard_runs

{reflectorch-1.4.0 → reflectorch-1.5.0}/CODE_OF_CONDUCT.md

@@ -1,12 +1,12 @@
-# Contributor Code of Conduct
-
-We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community. Examples of behavior that contributes to a positive environment for our community include:
-
-* Using welcoming and inclusive language
-* Being respectful of differing viewpoints and experiences
-* Gracefully accepting constructive criticism
-* Focusing on what is best for the community
-* Showing empathy towards other community members
-
-This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+# Contributor Code of Conduct
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community. Examples of behavior that contributes to a positive environment for our community include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 1.4, available at [http://contributor-covenant.org/version/1/4]

{reflectorch-1.4.0 → reflectorch-1.5.0}/CONTRIBUTING.md

@@ -1,28 +1,28 @@
-# Contributing to Reflectorch
-
-## 1. Reporting Issues
-
-If you encounter bugs, want to suggest features, or have questions, please open an issue using the [GitHub issue tracker](https://github.com/schreiber-lab/reflectorch/issues).
-
-When reporting a bug, please include:
-- A clear description of the issue
-- Steps to reproduce the bug (if applicable)
-- Any relevant error messages or screenshots
-
-## 2. Contributing Code
-
-To contribute code:
-
-1. **Fork** the repository.
-2. Make your changes in a new branch.
-3. Ensure your code is clear and well-documented.
-4. If applicable, add or update tests.
-5. Submit a [pull request](https://github.com/schreiber-lab/reflectorch/pulls) with a description of your changes.
-
-### Documentation
-
-If your changes affect user-facing features, please update the documentation accordingly. Documentation is built using [Jupyter Book](https://jupyterbook.org/). You can build it locally using:
-
-```bash
-jupyter-book build documentation
+# Contributing to Reflectorch
+
+## 1. Reporting Issues
+
+If you encounter bugs, want to suggest features, or have questions, please open an issue using the [GitHub issue tracker](https://github.com/schreiber-lab/reflectorch/issues).
+
+When reporting a bug, please include:
+- A clear description of the issue
+- Steps to reproduce the bug (if applicable)
+- Any relevant error messages or screenshots
+
+## 2. Contributing Code
+
+To contribute code:
+
+1. **Fork** the repository.
+2. Make your changes in a new branch.
+3. Ensure your code is clear and well-documented.
+4. If applicable, add or update tests.
+5. Submit a [pull request](https://github.com/schreiber-lab/reflectorch/pulls) with a description of your changes.
+
+### Documentation
+
+If your changes affect user-facing features, please update the documentation accordingly. Documentation is built using [Jupyter Book](https://jupyterbook.org/). You can build it locally using:
+
+```bash
+jupyter-book build documentation
 ```

{reflectorch-1.4.0 → reflectorch-1.5.0}/Dockerfile

@@ -1,13 +1,13 @@
-FROM nvidia/cuda:11.5.2-runtime-ubuntu20.04
-
-WORKDIR /app
-COPY . /app
-
-RUN apt-get update && \
-    pip3 install --upgrade pip && \
-    pip3 install --no-cache-dir -e '.[tests,docs,build]' && \
-    pip3 install --no-cache-dir jupyter
-
-EXPOSE 8888
-
+FROM nvidia/cuda:11.5.2-runtime-ubuntu20.04
+
+WORKDIR /app
+COPY . /app
+
+RUN apt-get update && \
+    pip3 install --upgrade pip && \
+    pip3 install --no-cache-dir -e '.[tests,docs,build]' && \
+    pip3 install --no-cache-dir jupyter
+
+EXPOSE 8888
+
 CMD ["jupyter", "notebook", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]

{reflectorch-1.4.0 → reflectorch-1.5.0}/LICENSE.txt

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2024 Reflectorch Developers
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+MIT License
+
+Copyright (c) 2024 Reflectorch Developers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.

{reflectorch-1.4.0 → reflectorch-1.5.0}/MANIFEST.in

@@ -1,15 +1,15 @@
-include configs/*
-exclude saved_models/*.pt
-exclude notebooks/*
-exclude paper/*
-exclude documentation/*
-exclude docs/*
-prune docs/*
-exclude .github/*
-
-include exp_data/data_C60.pt
-include exp_data/data_PTCDI-C3.pt
-include exp_data/data_C60.txt
-include exp_data/data_PTCDI-C3.txt
-include exp_data/33a.dat
+include configs/*
+exclude saved_models/*.pt
+exclude notebooks/*
+exclude paper/*
+exclude documentation/*
+exclude docs/*
+prune docs/*
+exclude .github/*
+
+include exp_data/data_C60.pt
+include exp_data/data_PTCDI-C3.pt
+include exp_data/data_C60.txt
+include exp_data/data_PTCDI-C3.txt
+include exp_data/33a.dat
 include exp_data/DIP-nSi_34a.dat