preppers 0.2.0__tar.gz

preppers-0.2.0/.github/workflows/CI.yml

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+# This file is autogenerated by maturin v1.7.8
+# with updates for CodeArtifact by @sjust-seerbio 2024-12-18
+#
+# To update, run
+#
+#    maturin generate-ci github -m python/Cargo.toml --pytest
+#
+# but be sure to preserve CodeArtifact behavior!
+#
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - master
+    tags:
+      - '*'
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: x86
+          - runner: ubuntu-22.04
+            target: aarch64
+          - runner: ubuntu-22.04
+            target: armv7
+          - runner: ubuntu-22.04
+            target: s390x
+          - runner: ubuntu-22.04
+            target: ppc64le
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+      - name: Run Rust unit tests
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+        run:
+          cargo test
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter --manifest-path python/Cargo.toml
+          sccache: 'true'
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+      - name: pytest
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+        shell: bash
+        run: |
+          set -e
+          python3 -m venv .venv
+          source .venv/bin/activate
+          pip install preppers --find-links dist --force-reinstall
+          pip install pytest
+          cd python && pytest
+      - name: pytest
+        if: ${{ !startsWith(matrix.platform.target, 'x86') && matrix.platform.target != 'ppc64' }}
+        uses: uraimo/run-on-arch-action@v2
+        with:
+          arch: ${{ matrix.platform.target }}
+          distro: ubuntu22.04
+          githubToken: ${{ github.token }}
+          install: |
+            apt-get update
+            apt-get install -y --no-install-recommends python3 python3-pip
+            pip3 install -U pip pytest
+          run: |
+            set -e
+            pip3 install preppers --find-links dist --force-reinstall
+            cd python && pytest
+
+  musllinux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-22.04
+            target: x86_64
+          - runner: ubuntu-22.04
+            target: x86
+          - runner: ubuntu-22.04
+            target: aarch64
+          - runner: ubuntu-22.04
+            target: armv7
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter --manifest-path python/Cargo.toml
+          sccache: 'true'
+          manylinux: musllinux_1_2
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-musllinux-${{ matrix.platform.target }}
+          path: dist
+      - name: pytest
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+        uses: addnab/docker-run-action@v3
+        with:
+          image: alpine:latest
+          options: -v ${{ github.workspace }}:/io -w /io
+          run: |
+            set -e
+            apk add py3-pip py3-virtualenv
+            python3 -m virtualenv .venv
+            source .venv/bin/activate
+            pip install preppers --no-index --find-links dist --force-reinstall
+            pip install pytest
+            cd python && pytest
+      - name: pytest
+        if: ${{ !startsWith(matrix.platform.target, 'x86') }}
+        uses: uraimo/run-on-arch-action@v2
+        with:
+          arch: ${{ matrix.platform.target }}
+          distro: alpine_latest
+          githubToken: ${{ github.token }}
+          install: |
+            apk add py3-virtualenv
+          run: |
+            set -e
+            python3 -m virtualenv .venv
+            source .venv/bin/activate
+            pip install pytest
+            pip install preppers --find-links dist --force-reinstall
+            cd python && pytest
+
+  windows:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: windows-latest
+            target: x64
+          - runner: windows-latest
+            target: x86
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+        if: ${{ startsWith(matrix.platform.target, 'x64') }}
+      - name: Run Rust unit tests
+        if: ${{ startsWith(matrix.platform.target, 'x64') }}
+        run:
+          cargo test
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+          architecture: ${{ matrix.platform.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter --manifest-path python/Cargo.toml
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+      - name: pytest
+        if: ${{ !startsWith(matrix.platform.target, 'aarch64') }}
+        shell: bash
+        run: |
+          set -e
+          python3 -m venv .venv
+          source .venv/Scripts/activate
+          pip install preppers --find-links dist --force-reinstall
+          pip install pytest
+          cd python && pytest
+
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: macos-15-intel
+            target: x86_64
+          - runner: macos-15
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Run Rust unit tests
+        run:
+            cargo test
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter --manifest-path python/Cargo.toml
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+      - name: pytest
+        run: |
+          set -e
+          python3 -m venv .venv
+          source .venv/bin/activate
+          pip install preppers --find-links dist --force-reinstall
+          pip install pytest
+          cd python && pytest
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist --manifest-path python/Cargo.toml
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: [self-hosted, aws-master, X64]
+    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
+    needs: [linux, musllinux, windows, macos, sdist]
+    permissions:
+      # Use to sign the release artifacts
+      id-token: write
+      # Used to upload release artifacts
+      contents: write
+      # Used to generate artifact attestation
+      attestations: write
+    steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - uses: actions/download-artifact@v4
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v1
+        with:
+          subject-path: 'wheels-*/*'
+      - name: Clear old pip creds
+        run: pip config unset global.index-url || true
+      - name: Log into AWS CodeArtifact
+        run: echo "MATURIN_PASSWORD=$(aws codeartifact get-authorization-token --domain seer --query authorizationToken --output text)" >> $GITHUB_ENV
+      - name: Publish to CodeArtifact
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_REPOSITORY_URL: https://seer-718843040700.d.codeartifact.us-west-2.amazonaws.com/pypi/seer_ds/
+          MATURIN_USERNAME: aws
+        with:
+          command: upload
+          args: --non-interactive --skip-existing wheels-*/*
+
+  pypi-release:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    if: ${{ startsWith(github.ref, 'refs/tags/') }}
+    needs: [linux, musllinux, windows, macos, sdist]
+    environment:
+      name: pypi
+      url: https://pypi.org/p/preppers
+    permissions:
+      contents: read
+      # Used for PyPI Trusted Publishing
+      id-token: write
+    steps:
+      - name: Download built distributions
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

preppers-0.2.0/.gitignore

@@ -0,0 +1,5 @@
+/target
+
+Cargo.lock
+
+.idea

preppers-0.2.0/Cargo.toml

@@ -0,0 +1,10 @@
+[package]
+name = "preppers"
+version = "0.2.0"
+edition = "2021"
+readme = "README.md"
+
+[dependencies]
+argh = "0.1.12"
+blart = "=0.3.0"
+fancy-regex = "0.17.0"

preppers-0.2.0/LICENSE.md

@@ -0,0 +1,209 @@
+**LICENSE**
+
+Use of the Fulcrum Pipeline™ framework software, including any portion
+thereof, is licensed under a Mandatory Grant-Back Apache 2.0 license, as
+modified by the Commons Clause (collectively, the "**License**").
+
+You may not use the Fulcrum Pipeline™ software, including any portion
+thereof, except in compliance with the License. See the entire License
+for specific language governing permissions and limitations under the
+License.
+
+------------------------------------------------------------------------
+
+**Mandatory Grant-Back** **Apache 2.0 License, as modified by the Commons Clause May 2026**
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+**1. Definitions**.
+
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+this document.
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+"**Legal Entity**" shall mean the union of the acting entity and all
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+"**You**" (or "**Your**") shall mean an individual or Legal Entity
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+"**Work**" shall mean the work of authorship, whether in Source or
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+**8. Limitation of Liability**. In no event and under no legal theory,
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preppers-0.2.0/PKG-INFO

@@ -0,0 +1,7 @@
+Metadata-Version: 2.4
+Name: preppers
+Version: 0.2.0
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: >=3.8

preppers-0.2.0/README.md

@@ -0,0 +1,82 @@
+<img alt="preppers logo" src="./static/preppers-logo.jpeg" height="128" align="left" style="margin: 8px">
+
+**Preppers** is a tool for *pr*otein to *pep*tide mapping, written in *R*u*s*t.
+It is designed for extreme speed and efficiency, using the *adaptive radix tree* implementation from [`blart`](https://github.com/declanvk/blart).
+
+## Usage
+
+### As a Python library
+
+For ease of use, Preppers includes Python bindings which can be installed
+from AWS CodeArtifact.
+
+To install, run:
+
+```shell
+aws codeartifact login --tool pip --repository seer_ds --domain seer --domain-owner 718843040700 --region us-west-2
+pip install preppers
+```
+
+and then in your Python code:
+
+```python
+import preppers
+```
+
+### As a command line tool
+
+**Coming soon!**
+
+For now, you can clone this repo and run:
+
+```shell
+cargo run --example annotate_fasta $PEPTIDES_FILE $FASTA_FILE
+```
+
+where `$PEPTIDES_FILE` is a file containing a list of peptides, one per line, and `$FASTA_FILE` is a FASTA file containing protein sequences.
+
+> [!TIP]
+> To set up a Rust environment, follow the instructions [here](https://www.rust-lang.org/tools/install).
+
+### As a Rust library
+
+To use Preppers in a Rust project, reference this repository in your `Cargo.toml`:
+
+```toml
+[dependencies]
+preppers = { git = "ssh://git@github.com/seerbio/preppers.git" }
+```
+
+## Running tests
+
+This package includes tests for functionality in Rust and Python.
+
+Rust tests:
+
+```shell
+cargo test
+```
+
+Python tests:
+```shell
+maturin develop --release -m python/Cargo.toml
+cd python
+pytest
+```
+
+> [!TIP]
+> For development, you will need to first install a Rust environment by following the instructions [here](https://www.rust-lang.org/tools/install).
+>
+> To install `maturin`, create a virtual environment and run `pip install maturin`.
+
+## Releasing a new version
+
+1. Update the version in `Cargo.toml` and `python/Cargo.toml`; these should match! Be sure to update the dependency version as well!
+
+> [!IMPORTANT]
+> Be sure to pick an appropriate [semantic version](https://semver.org/) for the new release!
+
+2. Commit the changes and push/merge to the `main` branch (this may require a PR).
+3. Create a new release in GitHub with the same version number using the format `vX.Y.Z`.
+   Click "auto-generate release notes" to automatically document merged PRs.
+4. GitHub Actions will automatically build and publish the new version to CodeArtifact.