fix: duplicates in ExpressionSet

.flake8

@@ -0,0 +1,19 @@
+[flake8]
+max-line-length = 125
+exclude =
+    __pycache__,
+    .git,
+    .tox,
+    build,
+    dist,
+    *.egg-info,
+    docs
+# E203: whitespace before ':' (conflicts with black)
+# W503: line break before binary operator (conflicts with black)
+# E402: module level import not at top of file
+# E722: do not use bare 'except'
+# F401: module imported but unused (acceptable in __init__.py for API exposure)
+# F403: 'from module import *' used (star imports)
+# F405: name may be undefined, or defined from star imports
+# F811: redefinition of unused name (often in try-except import blocks)
+extend-ignore = E203,W503,E402,E722,F401,F403,F405,F811

.github/workflows/ci.yml

@@ -0,0 +1,105 @@
+name: CI
+
+on:
+  push:
+    branches: [ master, main, develop ]
+  pull_request:
+    branches: [ master, main, develop ]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.9", "3.10", "3.11"]
+        exclude:
+          # Reduce matrix size for faster builds
+          - os: windows-latest
+            python-version: "3.9"
+          - os: macos-latest
+            python-version: "3.9"
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build pytest pytest-cov
+        pip install -e .[test]
+
+    - name: Run tests
+      run: |
+        pytest --cov=mewpy --cov-report=xml --cov-report=term-missing
+
+    - name: Upload coverage to Codecov
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10'
+      uses: codecov/codecov-action@v4
+      with:
+        file: ./coverage.xml
+        fail_ci_if_error: false
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 black isort
+        pip install -e .
+
+    - name: Lint with flake8
+      run: |
+        flake8 src tests
+
+    - name: Check formatting with black
+      run: |
+        black --check src tests
+
+    - name: Check import sorting with isort
+      run: |
+        isort --check-only src tests
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: |
+        python -m build
+
+    - name: Check package
+      run: |
+        twine check dist/*
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: dist-files
+        path: dist/

.github/workflows/main.yaml

@@ -3,13 +3,13 @@ name: CI-CD
 on:
   push:
     branches:
-    - devel
+    - dev
     tags:
     - '[0-9]+.[0-9]+.[0-9]+'
     - '[0-9]+.[0-9]+.[0-9]+a[0-9]+'
   pull_request:
     branches:
-    - devel
+    - dev
 
 jobs:
   test:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7]
+        python-version: [3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -33,6 +33,4 @@ jobs:
     - name: Test with tox
       run:
         tox -e py
-    - name: Report coverage
-      shell: bash
-      run: bash <(curl -s https://codecov.io/bash)
+

.gitignore

@@ -1,19 +1,177 @@
-.vscode/
-venv/
-__pycache__
-docs/build/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
 build/
-dist
-.idea
-mewpy.egg-info
-examples/models/gecko/eciML1515_batch.xml
-*.log
-.tox
-.eggs
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
 .coverage
-.pytest_cache
-htmlcov
-run_tox.sh
-tests/reports/
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/build/
+builddoc/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
 .ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be added to the global gitignore or merged into this project gitignore.  For a PyCharm
+#  project, it is generally recommended to include the .idea directory in version control.
+.idea/
+
+# VS Code
+.vscode/
+
+# macOS
 .DS_Store
+
+# Windows
+Thumbs.db
+ehthumbs.db
+Desktop.ini
+
+# Project specific
+tests/reports/
+examples/models/gecko/eciML1515_batch.xml
+run_tox.sh

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+     - requirements: docs/requirements.txt