partis-bcr 1.0.12.post1.dev1__tar.gz → 1.0.12.post1.dev2__tar.gz

partis_bcr-1.0.12.post1.dev2/.github/workflows/build.yml

@@ -0,0 +1,129 @@
+name: Build and Test
+
+on:
+  push:
+    branches: [ main, dev ]
+  pull_request:
+    branches: [ main, dev ]
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    env:
+      ACTIONS_ALLOW_UNSECURE_COMMANDS: true
+    steps:
+    - uses: actions/checkout@v3
+    - name: Checkout tags
+      run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
+    - name: Set git branch variable
+      run: echo ::set-env name=BRANCH::$(git branch --show-current)
+    - name: Set git tag variable
+      run: if [ $BRANCH == "main" ];then echo ::set-env name=TAG::$(git describe --tags);else echo ::set-env name=TAG::$BRANCH;fi
+    - name: Checkout submodules
+      shell: bash
+      run: |
+        auth_header="$(git config --local --get http.https://github.com/.extraheader)"
+        git submodule sync --recursive
+        git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
+    - name: Build the Docker image
+      run: docker build . -t quay.io/matsengrp/partis:$TAG
+    # - name: Run tests in the Docker image  # eh, would need to install simulation stuff to do this, and not worth it at the moment (the quick test is run at the end of the docker build above)
+    #   run: docker run quay.io/matsengrp/partis:$TAG /bin/bash -c "/partis/test/test.py --run-all"
+
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-13]
+        python-version: ['3.12']
+        install-method: ['pip', 'pipx']
+      fail-fast: false
+
+    env:
+      TERM: xterm
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    
+    - name: Checkout ham submodule
+      if: matrix.install-method == 'pip'
+      run: |
+        git submodule update --init packages/ham
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install system dependencies (Ubuntu)
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt update
+        sudo apt install -y python3 python3-pip python-is-python3 pipx build-essential cmake libgsl-dev libyaml-cpp-dev scons mafft ncurses-base ncurses-bin r-base
+        # sudo apt install libbpp-core libbpp-seq  # which packages do i actually have to write here?
+
+    - name: Install system dependencies (macOS)
+      if: startsWith(matrix.os, 'macos')
+      run: |
+        brew install python3 pipx cmake gsl yaml-cpp scons mafft r
+        # brew tap jydu/homebrew-biopp
+        # brew install libbpp-core bppsuite  # which packages do i actually have to write here?
+        brew install --cask font-lato
+
+    # - name: Install R tree generation packages  # could turn this back on, but it's really slow and not super important (and is unnecessary with --no-tree-gen arg below), although note we're still installing R above
+    #   run: |
+    #     R --slave -e 'dir.create(c(Sys.getenv("R_LIBS_USER")), recursive=TRUE); install.packages(c("TreeSim", "TreeSimGM", "geiger", "MASS"), repos="http://cran.rstudio.com/", dependencies=TRUE, lib=c(Sys.getenv("R_LIBS_USER")))'
+
+    - name: Install with pip
+      if: matrix.install-method == 'pip'
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -e . -v
+
+    - name: Install with pipx
+      if: matrix.install-method == 'pipx'
+      run: |
+        pipx install partis-bcr
+
+    - name: Test partis help
+      run: |
+        partis --help
+
+    - name: Test scripts work
+      run: |
+        split-loci.py --help
+
+    - name: Run quick test
+      run: |
+        partis-test.py --quick
+
+    - name: Run full test
+      run: |
+        # if [[ "${{ matrix.install-method }}" == "pipx" || "${{ matrix.os }}" == macos* ]]; then
+        if "${{ matrix.os }}" == macos* ]]; then
+          partis-test.py --no-simu
+          partis-test.py --paired --no-simu
+        else
+          partis-test.py --no-per-base-mutation --no-tree-gen
+          partis-test.py --paired --no-per-base-mutation --no-tree-gen
+        fi
+
+    - name: Build and publish to PyPI
+      if: matrix.install-method == 'pip' && github.event_name == 'push'  #  && github.ref == 'refs/heads/main'  #  && matrix.os == 'ubuntu-latest'
+      run: |
+        python -m pip install build twine
+        if [ "${{ matrix.os }}" = "ubuntu-latest" ]; then
+          python setup.py bdist_wheel --plat-name manylinux1_x86_64
+          python -m build --sdist 2>&1 | grep -v 'adding .test/\|adding .data/\|creating partis_bcr.*/test/\|copying docs/\|copying data/\|copying packages/\|copying python/.*/test/\|copying build/.*/test/'
+          python -m twine check dist/*
+          python -m twine upload dist/*
+        else
+          python -m build --wheel 2>&1 | grep -v 'adding .test/\|adding .data/\|creating partis_bcr.*/test/\|copying docs/\|copying data/\|copying packages/\|copying python/.*/test/\|copying build/.*/test/'
+          python -m twine check dist/*.whl
+          python -m twine upload dist/*.whl
+        fi
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}

partis_bcr-1.0.12.post1.dev2/PKG-INFO

@@ -0,0 +1,87 @@
+Metadata-Version: 2.4
+Name: partis-bcr
+Version: 1.0.12.post1.dev2
+Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
+Home-page: https://github.com/psathyrella/partis
+Author: Duncan Ralph
+Author-email: dkralph@gmail.com
+License: GPL-3.0-or-later
+Project-URL: Bug Reports, https://github.com/psathyrella/partis/issues
+Project-URL: Source, https://github.com/psathyrella/partis
+Project-URL: Documentation, https://github.com/psathyrella/partis/tree/main/docs
+Keywords: immunology bioinformatics bcr tcr antibody sequence-analysis
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: COPYING
+Requires-Dist: biopython
+Requires-Dist: colored-traceback
+Requires-Dist: dendropy
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: psutil
+Requires-Dist: pysam
+Requires-Dist: PyYAML
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: six
+Provides-Extra: plotting
+Requires-Dist: circlify; extra == "plotting"
+Requires-Dist: ete3; extra == "plotting"
+Requires-Dist: joypy; extra == "plotting"
+Requires-Dist: matplotlib; extra == "plotting"
+Provides-Extra: full
+Requires-Dist: circlify; extra == "full"
+Requires-Dist: ete3; extra == "full"
+Requires-Dist: joypy; extra == "full"
+Requires-Dist: levenshtein; extra == "full"
+Requires-Dist: matplotlib; extra == "full"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+[![](https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic)](https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html)
+### partis
+
+Partis is an HMM-based framework for B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction.
+It is built on top of the [ham](https://github.com/psathyrella/ham) HMM compiler and [ig-sw](https://github.com/matsengrp/ig-sw) set of Smith-Waterman annotation tools.
+Partis is free software under the GPL v3.
+
+The various components are described in the following papers.
+Since they do quite different things, it's best if you can cite the specific paper(s) that describe the components that you're using.
+
+  * [Paired clustering](https://doi.org/10.1371/journal.pcbi.1010723) Ralph, DK, & Matsen IV, FA (2022). _Inference of B cell clonal families using heavy/light chain pairing information._ PLoS Computational Biology, 18(11), e1010723.
+  * [Selection metrics](https://doi.org/10.1371/journal.pcbi.1008391) Ralph, DK, & Matsen IV, FA (2020). _Using B cell receptor lineage structures to predict affinity._ PLoS Computational Biology, 16(11), e1008391.
+  * [Germline inference](https://doi.org/10.1371/journal.pcbi.1007133) Ralph, DK, & Matsen IV, FA (2019). _Per-sample immunoglobulin germline inference \[...\]._ PLoS Computational Biology, 15(7), e1007133.
+  * [Clonal family inference](http://dx.doi.org/10.1371/journal.pcbi.1005086) Ralph, DK, & Matsen IV, FA (2016). _Likelihood-based Inference of B-cell Clonal Families._ PLoS Computational Biology, 12(10), e1005086.
+  * [HMM framework and BCR annotation](http://doi.org/10.1371/journal.pcbi.1004409) Ralph, DK, & Matsen IV, FA (2016). _Consistency of \[...\] Enables Accurate B Cell Receptor Sequence Annotation._ PLoS Computational Biology, 12(1), e1004409.
+
+The best place to start reading the manual is either [installation](docs/install.md) or [quick start](docs/quick-start.md), but there's also a [table of contents](docs/contents.md).
+Details on the many options not documented there may be found by running each subcommand's help, for instance `partis cache-parameters --help` or `partis simulate --help`.
+
+To ask questions about how to run or how things work, please use the [google group](https://groups.google.com/g/partis).
+For specific issues with the software, e.g. bug reports or feature requests, on the other hand, [submit an issue](https://github.com/psathyrella/partis/issues/new) on github.
+You can also search through past discussion both on the google group and in [closed issues](https://github.com/psathyrella/partis/issues?q=is%3Aissue+is%3Aclosed).
+If you'd like to be notified when something important changes, please subscribe to the google group.

partis_bcr-1.0.12.post1.dev2/partis_bcr.egg-info/PKG-INFO

@@ -0,0 +1,87 @@
+Metadata-Version: 2.4
+Name: partis-bcr
+Version: 1.0.12.post1.dev2
+Summary: B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference
+Home-page: https://github.com/psathyrella/partis
+Author: Duncan Ralph
+Author-email: dkralph@gmail.com
+License: GPL-3.0-or-later
+Project-URL: Bug Reports, https://github.com/psathyrella/partis/issues
+Project-URL: Source, https://github.com/psathyrella/partis
+Project-URL: Documentation, https://github.com/psathyrella/partis/tree/main/docs
+Keywords: immunology bioinformatics bcr tcr antibody sequence-analysis
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: COPYING
+Requires-Dist: biopython
+Requires-Dist: colored-traceback
+Requires-Dist: dendropy
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: psutil
+Requires-Dist: pysam
+Requires-Dist: PyYAML
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: six
+Provides-Extra: plotting
+Requires-Dist: circlify; extra == "plotting"
+Requires-Dist: ete3; extra == "plotting"
+Requires-Dist: joypy; extra == "plotting"
+Requires-Dist: matplotlib; extra == "plotting"
+Provides-Extra: full
+Requires-Dist: circlify; extra == "full"
+Requires-Dist: ete3; extra == "full"
+Requires-Dist: joypy; extra == "full"
+Requires-Dist: levenshtein; extra == "full"
+Requires-Dist: matplotlib; extra == "full"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+[![](https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic)](https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html)
+### partis
+
+Partis is an HMM-based framework for B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction.
+It is built on top of the [ham](https://github.com/psathyrella/ham) HMM compiler and [ig-sw](https://github.com/matsengrp/ig-sw) set of Smith-Waterman annotation tools.
+Partis is free software under the GPL v3.
+
+The various components are described in the following papers.
+Since they do quite different things, it's best if you can cite the specific paper(s) that describe the components that you're using.
+
+  * [Paired clustering](https://doi.org/10.1371/journal.pcbi.1010723) Ralph, DK, & Matsen IV, FA (2022). _Inference of B cell clonal families using heavy/light chain pairing information._ PLoS Computational Biology, 18(11), e1010723.
+  * [Selection metrics](https://doi.org/10.1371/journal.pcbi.1008391) Ralph, DK, & Matsen IV, FA (2020). _Using B cell receptor lineage structures to predict affinity._ PLoS Computational Biology, 16(11), e1008391.
+  * [Germline inference](https://doi.org/10.1371/journal.pcbi.1007133) Ralph, DK, & Matsen IV, FA (2019). _Per-sample immunoglobulin germline inference \[...\]._ PLoS Computational Biology, 15(7), e1007133.
+  * [Clonal family inference](http://dx.doi.org/10.1371/journal.pcbi.1005086) Ralph, DK, & Matsen IV, FA (2016). _Likelihood-based Inference of B-cell Clonal Families._ PLoS Computational Biology, 12(10), e1005086.
+  * [HMM framework and BCR annotation](http://doi.org/10.1371/journal.pcbi.1004409) Ralph, DK, & Matsen IV, FA (2016). _Consistency of \[...\] Enables Accurate B Cell Receptor Sequence Annotation._ PLoS Computational Biology, 12(1), e1004409.
+
+The best place to start reading the manual is either [installation](docs/install.md) or [quick start](docs/quick-start.md), but there's also a [table of contents](docs/contents.md).
+Details on the many options not documented there may be found by running each subcommand's help, for instance `partis cache-parameters --help` or `partis simulate --help`.
+
+To ask questions about how to run or how things work, please use the [google group](https://groups.google.com/g/partis).
+For specific issues with the software, e.g. bug reports or feature requests, on the other hand, [submit an issue](https://github.com/psathyrella/partis/issues/new) on github.
+You can also search through past discussion both on the google group and in [closed issues](https://github.com/psathyrella/partis/issues?q=is%3Aissue+is%3Aclosed).
+If you'd like to be notified when something important changes, please subscribe to the google group.