spectrseqtools 0.1.0__tar.gz

spectrseqtools-0.1.0/.github/workflows/ci.yml

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+name: test
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  fmt:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: prefix-dev/setup-pixi@v0
+
+      - run: |
+          pixi run format --check
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: prefix-dev/setup-pixi@v0
+
+      - run: |
+          pixi run lint
+
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: prefix-dev/setup-pixi@v0
+
+      - run: |
+          pixi run test -v

spectrseqtools-0.1.0/.github/workflows/conventional_prs.yml

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+name: PR
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  title-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v3.4.0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

spectrseqtools-0.1.0/.github/workflows/release_please.yml

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+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+permissions:
+  contents: write
+  issues: write
+  pull-requests: write
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    outputs:
+      release_created: ${{ steps.release.outputs.release_created }}
+    steps:
+      - uses: GoogleCloudPlatform/release-please-action@v3
+        id: release
+        with:
+          release-type: python
+          package-name: spectrseqtools
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: release-please
+    if: ${{ needs.release-please.outputs.release_created }}
+    permissions:
+      id-token: write
+    environment:
+      name: pypi
+      url: https://pypi.org/p/spectrseqtools
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
+
+      - name: Build source and wheel distribution + check build
+        run: |
+          pixi run -e dev check-build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

spectrseqtools-0.1.0/.gitignore

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+__pycache__
+.idea
+.pytest_cache
+poetry.lock
+*.DS_Store
+*gurobi.log
+*.code-workspace
+tests/self_test*
+tests/testcases/*/fragments.plot.html
+tests/testcases/*/fragments.plot.end.html
+tests/testcases/*/fragments.plot.internal.html
+tests/testcases/*/fragments.plot.start.html
+tests/testcases/*/fragments.raw
+tests/testcases/*/fragments.singletons.tsv
+tests/testcases/*/fragments.standard_unit_fragments.tsv
+tests/testcases/*/fragments.testing.meta.yaml
+tests/scratch_*

spectrseqtools-0.1.0/CHANGELOG.md

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+# Changelog
+
+## 0.1.0 (2026-01-30)
+
+
+### Features
+
+* add modification rate ([#12](https://github.com/spectrseq/spectrseqtools/issues/12)) ([450e586](https://github.com/spectrseq/spectrseqtools/commit/450e586c6a764e3098300b2ffc95b3146d8e5d26))
+* add option to set lp time limits ([#40](https://github.com/spectrseq/spectrseqtools/issues/40)) ([555eef7](https://github.com/spectrseq/spectrseqtools/commit/555eef7703a4af3b30f5e96ca8124dadb153bdd3))
+* add option to set output directory ([#44](https://github.com/spectrseq/spectrseqtools/issues/44)) ([0119188](https://github.com/spectrseq/spectrseqtools/commit/0119188753e54c1e6114b3e0b8adecf2353ce850))
+* add preprocessing ([#21](https://github.com/spectrseq/spectrseqtools/issues/21)) ([40c5214](https://github.com/spectrseq/spectrseqtools/commit/40c521476289f6e6a017c5f3ba81a55c0faf0fbf))
+* additionally output sequence with all alternate nucleotides ([#42](https://github.com/spectrseq/spectrseqtools/issues/42)) ([675a310](https://github.com/spectrseq/spectrseqtools/commit/675a31004fd52d751640fdeaa43b4a533c8d13d6))
+* allow both raw and preprocessed data as input ([#23](https://github.com/spectrseq/spectrseqtools/issues/23)) ([d4d353a](https://github.com/spectrseq/spectrseqtools/commit/d4d353a97f1d95f0b171e9cbd4e2a5b5096ec7ba))
+* allow singleton selection for tsv input ([#29](https://github.com/spectrseq/spectrseqtools/issues/29)) ([0beb9cd](https://github.com/spectrseq/spectrseqtools/commit/0beb9cd7bd740d67f98cea38011ac62cc2df2e4c))
+* allow using lp based filter on terminal fragments ([#45](https://github.com/spectrseq/spectrseqtools/issues/45)) ([fac53a6](https://github.com/spectrseq/spectrseqtools/commit/fac53a6bc331617b5671205a7bbb21e5635fb8b0))
+* build skeleton and use that to constrain the MILP ([15b21bd](https://github.com/spectrseq/spectrseqtools/commit/15b21bd1f7b439d7f48ff0c41bdf8c660c061177))
+* enable recomputing of dp table ([#22](https://github.com/spectrseq/spectrseqtools/issues/22)) ([5f7ffd7](https://github.com/spectrseq/spectrseqtools/commit/5f7ffd75edeefa13fd4c52f34b368af117bdc20c))
+* establish standard unit masses for simplified nucleotide consideration ([#15](https://github.com/spectrseq/spectrseqtools/issues/15)) ([ab5206d](https://github.com/spectrseq/spectrseqtools/commit/ab5206d5a0ade3e9db03dd86338cd7e4ca5c4d94))
+* estimate sequence length ([#20](https://github.com/spectrseq/spectrseqtools/issues/20)) ([a6bc2d6](https://github.com/spectrseq/spectrseqtools/commit/a6bc2d60dd01d578e5c9107d7ff5f678865d3657))
+* explain observed masses or mass differences using dynamic programming ([#3](https://github.com/spectrseq/spectrseqtools/issues/3)) ([c36b8cc](https://github.com/spectrseq/spectrseqtools/commit/c36b8cc474194e5f6f9ec129318af14507de10b9))
+* extend dp to nucleotides ([#9](https://github.com/spectrseq/spectrseqtools/issues/9)) ([0b5f411](https://github.com/spectrseq/spectrseqtools/commit/0b5f411edac2f6e88ec46700fb438638623a0e82))
+* filter early retention times with noise peaks ([#32](https://github.com/spectrseq/spectrseqtools/issues/32)) ([b7b1301](https://github.com/spectrseq/spectrseqtools/commit/b7b130113844397d42eeb14c09abdec303e09712))
+* filter fragments with lp ([#10](https://github.com/spectrseq/spectrseqtools/issues/10)) ([0b947fc](https://github.com/spectrseq/spectrseqtools/commit/0b947fc04a267bf7ed8ab76fd27ff934f9bd49a3))
+* filter fragments with sequence mass ([#16](https://github.com/spectrseq/spectrseqtools/issues/16)) ([d51e573](https://github.com/spectrseq/spectrseqtools/commit/d51e5733b2963a1cce827527c3fc1f5bb1f12626))
+* group same-weight fragments during skeleton building ([#17](https://github.com/spectrseq/spectrseqtools/issues/17)) ([e3d34f5](https://github.com/spectrseq/spectrseqtools/commit/e3d34f57b3361de11529339c5fa1cbf5a9b33ece))
+* improve sequence length estimation with lp based selection ([#26](https://github.com/spectrseq/spectrseqtools/issues/26)) ([b102ffb](https://github.com/spectrseq/spectrseqtools/commit/b102ffbd844a73191cd379d111aa085ce501c544))
+* plot different fragment classes individually ([#46](https://github.com/spectrseq/spectrseqtools/issues/46)) ([281a848](https://github.com/spectrseq/spectrseqtools/commit/281a84802ad6d8d0c11f745cdafad7445676afd5))
+* reduce alphabet after skeleton building ([#19](https://github.com/spectrseq/spectrseqtools/issues/19)) ([4e95659](https://github.com/spectrseq/spectrseqtools/commit/4e95659685b1e07b5bf3cb94c2d285ff867c2e9c))
+* set intensity cutoff based on percentile ([#41](https://github.com/spectrseq/spectrseqtools/issues/41)) ([cfc1085](https://github.com/spectrseq/spectrseqtools/commit/cfc1085f096f55439e2b6999fe7f8ea28ba22261))
+
+
+### Bug Fixes
+
+* allow using cli ([#13](https://github.com/spectrseq/spectrseqtools/issues/13)) ([09a65af](https://github.com/spectrseq/spectrseqtools/commit/09a65afa989d3912715505a209e35ed6cab7154a))
+* catch exceptions during lp initialization for ambiguity removal ([#39](https://github.com/spectrseq/spectrseqtools/issues/39)) ([4bf108b](https://github.com/spectrseq/spectrseqtools/commit/4bf108b2e415d1c1edfd8e95061d21651555ff28))
+* catch exceptions if no prediction is possible ([#30](https://github.com/spectrseq/spectrseqtools/issues/30)) ([02405e1](https://github.com/spectrseq/spectrseqtools/commit/02405e16f53a72a5424232f1d8f18d001934c05d))
+* catch exceptions while solving lp ([#38](https://github.com/spectrseq/spectrseqtools/issues/38)) ([7ea9737](https://github.com/spectrseq/spectrseqtools/commit/7ea97376bb708adf9abd93864191057a1b0d08da))
+* catch nonetype bases during lp evaluation ([#37](https://github.com/spectrseq/spectrseqtools/issues/37)) ([4c5c695](https://github.com/spectrseq/spectrseqtools/commit/4c5c695fc16af46b99765e13fa3d69adb0ed9371))
+* ensure correct fragment end indices for lp ([#25](https://github.com/spectrseq/spectrseqtools/issues/25)) ([051e744](https://github.com/spectrseq/spectrseqtools/commit/051e7448d0bb32747d83ec5b7966df701c7cfed5))
+* ensure usage of correct singleton path ([#35](https://github.com/spectrseq/spectrseqtools/issues/35)) ([51264eb](https://github.com/spectrseq/spectrseqtools/commit/51264eb74d65533955781064bcbc99309a408441))
+* filter singletons by combined tag mass ([#24](https://github.com/spectrseq/spectrseqtools/issues/24)) ([7b6ab9a](https://github.com/spectrseq/spectrseqtools/commit/7b6ab9a04282f706eebaa56ca5b625e313efd2e5))
+* map singletons to mass representative to avoid filtering them out ([#33](https://github.com/spectrseq/spectrseqtools/issues/33)) ([82de7e8](https://github.com/spectrseq/spectrseqtools/commit/82de7e88b4971c6f2d198d5ae12c6a4b20427bc8))
+* plot only one base at each position of global sequence ([#34](https://github.com/spectrseq/spectrseqtools/issues/34)) ([f6ec9a2](https://github.com/spectrseq/spectrseqtools/commit/f6ec9a2880b3fa35cccacbdb6aa5189455c58c11))
+* skip fragments with non-explainable masses during ladder building; allow start fragments to reach the end, and vice versa; non certain start or end fragments may also touch start and end and even span the entire sequence ([#7](https://github.com/spectrseq/spectrseqtools/issues/7)) ([9a1f03b](https://github.com/spectrseq/spectrseqtools/commit/9a1f03b5c6eb243399c495ac3463d201dfd04a7b))
+
+
+### Performance Improvements
+
+* further limit MILP by terminal fragment ladder skeleton ([6e9b7aa](https://github.com/spectrseq/spectrseqtools/commit/6e9b7aa97f3a094b4cbecbb2f2721c2abd444893))