Merge pull request #1 from valentingol/dev

Initial commit

.flake8

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+[flake8]
+max-line-length = 88
+extend-ignore = E203
+exclude = dinosor/_version.py

.github/workflows/flake.yaml

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+name: Flake 8
+
+on: [push]
+
+jobs:
+  flake-lint:
+    runs-on: ubuntu-latest
+    name: Flake Lint
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v2
+      - name: Set up Python environment
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Lint
+        uses: py-actions/flake8@v2
+        with:
+          label: Flake

.github/workflows/mypy.yaml

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+name: MyPy
+
+on: [push]
+
+jobs:
+  mypy-lint:
+    runs-on: ubuntu-latest
+    name: MyPy Lint
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v2
+      - name: Mypy Check
+        run: |
+          python -m pip install --upgrade pip
+          pip install mypy==1.1.1 mypy-extensions==1.0.0
+          python -m pip install types-PyYAML
+          mypy --install-types --non-interactive --config-file pyproject.toml .

.github/workflows/pydocstyle.yaml

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+name: Pydocstyle
+
+on: [push]
+
+jobs:
+  pydoc-lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.9
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          pip install pydocstyle
+          pip install -e .
+      - name: Analysing the code with pydocstyle
+        run: |
+          pydocstyle --convention=numpy . | tee pydocstyle.txt
+      - name: Check the number of errors
+        run: |
+          n_errors=$(wc -l < pydocstyle.txt)
+          echo "Number of errors in docstrings: $n_errors"
+          python github_actions_utils/pydocstyle_manager.py --n_errors=$n_errors

.github/workflows/ruff.yaml

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+name: Ruff
+
+on: [push]
+
+jobs:
+  ruff-lint:
+    runs-on: ubuntu-latest
+    name: Ruff Lint
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v2
+      - name: Set up Python environment
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Lint
+        uses: jpetrucciani/ruff-check@main

.gitignore

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+# Cache
+**_cache
+**.pyc
+*/__pycache__
+# Env
+.env
+.venv
+env
+env.yaml
+environment.yml
+venv
+**.egg-info
+# VScode
+.vscode
+# Temporary files
+**/tmp.py
+**/tmp.ipynb
+# Tests
+.coverage
+# SCM
+src/torch_pca/_version.py
+# Doc
+build
+docs/_build

.markdownlint.json

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+{
+    "MD013": {
+        "line_length": 120
+    },
+    "MD034": false
+}

.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+
+-   repo: https://github.com/pycqa/flake8
+    rev: '4.0.1'
+    hooks:
+    -   id: flake8
+
+-   repo: https://github.com/pycqa/pydocstyle
+    rev: '6.1.1'
+    hooks:
+    -   id: pydocstyle
+        args:
+        - --convention=numpy

.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+sphinx:
+  configuration: docs/conf.py
+
+formats:
+  - pdf
+  - epub
+
+python:
+  install:
+    - requirements: docs/requirements.txt

CONTRIBUTING.md

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+# Contributing to My Worflow Template
+
+Everyone can contribute to Pytorch PCA, and we value everyone’s contributions.
+There are several ways to contribute, including:
+
+- Raising [issue](https://github.com/valentingol/torch_pca/issues)
+  on the Github repository
+
+- Proposing [Pull requests](https://github.com/valentingol/torch_pca/pulls)
+  to the Github repository
+
+- Contact me by email (valentin.goldite@gmail.com)
+
+- Create your own repository based on this one and cite it
+
+## Pull request checklist
+
+Before proposing a PR you must follow some rule:
+
+- Pull requests typically comprise a **single git commit**. In preparing a pull
+  request for review, you may need to squash together multiple commits.
+
+- Code should work on Python 3.8-3.11
+
+- Code should respect [PEP8](https://peps.python.org/pep-0008/)
+
+- The format of the docstrings follows [Numpy guidline](https://numpydoc.readthedocs.io/en/latest/format.html)
+
+- It is recommended to use all linters listed in `requirements-dev.txt`
+
+Before submitting a PR you should run this pipeline:
+
+```script
+sh checks.sh
+```
+
+**Try to not decrease the global Pylint score** after a pull request. A minimum
+of 7.0/10.0 is required but **we preferably want above 9.0/10.0.**
+
+## Commit message
+
+Commits should start with an emoji and directly followed by a descriptive and
+precise message that starts with a capital letter and should be written in present
+tense. E.g:
+
+*✨: added configuration function* ❌ Bad
+
+*✨ Add function to save configuration file* ✅ Good
+
+Emojis not only look great but also makes you rethink what to add to a commit.
+The goal is to dedicate each single kind of change to a single commit. Make many
+but small commits!
+
+Emojis of commit message follow mainly the [Gitmoji](https://gitmoji.dev/) guideline
+(the different ones start with an asterisk *). The most useful are:
+
+| Emoji                                 | Description                                             |
+| ------------------------------------- | ------------------------------------------------------- |
+| 🎉 `:tada:`                            | Initial commit                                          |
+| ✨ `:sparkles:`                        | New cool feature                                        |
+| ➕ `:heavy_plus_sign:` *               | Add file and/or folder                                  |
+| 🔥 `:fire:`                            | Remove some code or file                                |
+| 📝 `:memo:`                            | Add or improve readme, docstring or comments            |
+| 🐛 `:bug:`                             | Fix a bug                                               |
+| 🎨 `:art:`                             | Improve style, or format the code                       |
+| ♻️ `:recycle:`                         | Refactor the code                                       |
+| 🚚 `:truck:`                           | Rename and/or move files and folders                    |
+| 🏗️ `:building_construction:`           | Change a part of the repository architecture            |
+| ✏️  `:pencil2:`                        | Fix typo                                                |
+| ⚙️  `:gear:` *                         | Add or update configuration file (config/exp.yaml, ...) |
+| 🔧 `:wrench:`                          | Add or update tool configuration (pyproject.toml, ...)  |
+| 🍱 `:bento:`                           | Add or update assets                                    |
+| 🚀 `:rocket:` *                        | Improve performance                                     |
+| ⚗️ `:alembic:`                         | Perform experiment                                      |
+| 🚸 `:children_crossing:`               | Improve user experience                                 |
+| 🆙 `:up:` * OR 🔖 `:bookmark:`          | Update the version/tag                                  |
+| ⬆️  `:arrow_up:`                       | Upgrade dependency                                      |
+| 🚧 `:construction:`                    | Work in progress                                        |
+| 🔀 `:twisted_rightwards_arrows:`       | Merge a branch                                          |
+| Check [Gitmoji](https://gitmoji.dev/) | *OTHER*                                                 |
+
+Installing the [Gitmoji VSCode extension](https://marketplace.visualstudio.com/items?itemName=seatonjiang.gitmoji-vscode)
+can be useful to get the emoji you want quickly.
+
+## Version and tag numbers
+
+Version/tag numbers will be assigned according to the [Semantic Versioning scheme](https://semver.org/).
+This means, given a version number MAJOR.MINOR.PATCH, we will increment the:
+
+- MAJOR version when we make incompatible API changes
+- MINOR version when we add functionality in a backwards compatible manner
+- PATCH version when we make backwards compatible bug fixes

README.md

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-# torch_pca
-Principal Component Anlaysis (PCA) in PyTorch.
+# Pytorch CPA
+
+Principal Component Anlaysis (PCA) in PyTorch. The intention is to provide a
+simple and easy to use implementation of PCA in PyTorch, the most similar to
+the `sklearn`'s PCA as possible (in terms of API and, of course, output).
+
+![PythonVersion](https://img.shields.io/badge/python-3.8%20%7E%203.11-informational)
+![PytorchVersion](https://img.shields.io/badge/pytorch-1.8%20%7E%201.13%20%7C%202.0+-informational)
+
+[![GitHub User followers](https://img.shields.io/github/followers/valentingol?label=User%20followers&style=social)](https://github.com/valentingol)
+[![GitHub User's User stars](https://img.shields.io/github/stars/valentingol?label=User%20Stars&style=social)](https://github.com/valentingol)
+
+[![Ruff_logo](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
+[![Black_logo](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+[![Ruff](https://github.com/valentingol/torch_pca/actions/workflows/ruff.yaml/badge.svg)](https://github.com/valentingol/Dinosor/actions/workflows/ruff.yaml)
+[![Flake8](https://github.com/valentingol/torch_pca/actions/workflows/flake.yaml/badge.svg)](https://github.com/valentingol/Dinosor/actions/workflows/flake.yaml)
+[![Pydocstyle](https://github.com/valentingol/torch_pca/actions/workflows/pydocstyle.yaml/badge.svg)](https://github.com/valentingol/Dinosor/actions/workflows/pydocstyle.yaml)
+[![MyPy](https://github.com/valentingol/torch_pca/actions/workflows/mypy.yaml/badge.svg)](https://github.com/valentingol/Dinosor/actions/workflows/mypy.yaml)
+
+## Installation
+
+```bash
+pip install torch-cpa
+```
+
+## How to use
+
+```python
+from torch_cpa import PCA
+
+# Create like sklearn.decomposition.PCA
+pca_model = PCA(n_components=None, whiten=False)
+
+# Use like sklearn.decomposition.PCA
+>>> new_X1 = pca_model.fit_transform(X1)
+>>> new_X2 = pca_model.transform(X2)
+>>> print(pca.explained_variance_ratio_)
+[0.756, 0.142, 0.062, ...]
+```

checks.sh

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+# Style constants
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+WHITE='\033[0m'
+BOLD=$(tput bold)
+NORMAL=$(tput sgr0)
+
+# Check output function
+check_output() {
+    if [ $? -ne 0 ]; then
+        echo "${RED}$1 fail!\nExit${WHITE}"
+        exit 1
+    else
+        echo "${GREEN}$1 pass${WHITE}\n"
+    fi
+}
+
+# Checks
+echo "**************** Typing ****************"
+mypy .
+check_output "Typing checks"
+
+echo "************* Import order *************"
+isort --check-only .
+check_output "Import order checks"
+
+echo "***************** PEP8 *****************"
+flake8 .
+check_output "PEP8 checks"
+
+echo "***************** Ruff *****************"
+ruff .
+check_output "Ruff checks"
+
+echo "*********** Style evaluation ***********"
+score=$(pylint . | sed -n 's/^Your code has been rated at \([-0-9.]*\)\/.*/\1/p')
+
+echo "Pylint score: ${BOLD}$score/10.0${NORMAL} (details by running: pylint .)\nMinimum authorized score: 7.0\n"
+
+echo "************** Unit tests **************"
+pytest --cov-report term-missing --cov=./src tests/
+check_output "Unit tests"
+
+printf "\n${GREEN}${BOLD}All checks pass${NORMAL}${WHITE}\n\n"

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = ../docs
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)