fun-proteomics 0.5.0__tar.gz

fun_proteomics-0.5.0/.gitattributes

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+*.py text eol=lf
+*.R text eol=lf
+*.nf text eol=lf
+*.config text eol=lf
+*.workflow text eol=lf
+*.tsv text eol=lf
+*.md text eol=lf

fun_proteomics-0.5.0/.github/workflows/publish.yml

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+name: Publish Python package
+on:
+  workflow_dispatch:
+permissions:
+  contents: read
+jobs:
+  build_and_test:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Build checked distributions
+        run: |
+          python -m pip install build twine
+          python -m build
+          python -m twine check dist/*
+          python scripts/validate_distribution.py
+          python -m pip install dist/*.whl
+          sudo apt-get update
+          sudo apt-get install -y r-base r-bioc-limma r-bioc-edger r-cran-jsonlite
+      - name: Test the installed package
+        env:
+          FUN_PROTEOMICS_TEST_INSTALLED: '1'
+          PROTEOMICS_RSCRIPT: /usr/bin/Rscript
+        run: |
+          python -m unittest discover -s tests -p test_package_cli.py -v
+          python tests/run_package_smoke.py
+      - uses: actions/upload-artifact@v4
+        with:
+          name: python-distributions
+          path: dist/
+  publish:
+    needs: build_and_test
+    runs-on: ubuntu-24.04
+    environment:
+      name: pypi
+      url: https://pypi.org/project/fun-proteomics/
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: python-distributions
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1

fun_proteomics-0.5.0/.github/workflows/validate.yml

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+name: Validate PASEF Proteomics
+on: [push, pull_request]
+jobs:
+  source_and_synthetic_pipeline:
+    runs-on: ubuntu-24.04
+    env:
+      PROTEOMICS_RSCRIPT: /usr/bin/Rscript
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install locked runtime
+        run: bash setup_environment.sh
+      - name: Install R and statistical dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y r-base r-base-dev python3.12 python3.12-venv libcurl4-openssl-dev libssl-dev libxml2-dev
+          bash scripts/install_differential_tools.sh /usr/bin/Rscript
+      - name: Validate semantics and publication exclusions
+        run: |
+          .runtime/env/bin/python -m unittest discover -s tests -v
+          .runtime/env/bin/python scripts/validate_repo.py
+      - name: Check Nextflow and synthetic end-to-end execution
+        run: |
+          export PATH="$PWD/.runtime/env/bin:$PATH"
+          export JAVA_HOME="$PWD/.runtime/env"
+          export NXF_HOME="$PWD/.runtime/nextflow"
+          export NXF_VER=26.04.2
+          export NXF_DISABLE_CHECK_LATEST=true
+          nextflow lint main.nf
+          bash tests/run_smoke.sh
+          export PROTEOMICS_DIA_PYTHON=/usr/bin/python3.12
+          /usr/bin/python3.12 tests/run_diapasef_smoke.py
+# Synthetic tests contain no spectra or registered tool binaries.
+# Real searches require user-supplied data and individually registered software.
+
+  dia_quantification:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Install pinned DIA reporting dependencies
+        run: pip install -r modules/diapasef/requirements-lock.txt
+      - name: Install intensity statistics
+        run: sudo apt-get update && sudo apt-get install -y r-base r-bioc-limma r-bioc-edger r-cran-jsonlite
+      - name: Check real reporting code on synthetic DIA reports
+        env:
+          PROTEOMICS_RSCRIPT: /usr/bin/Rscript
+        run: |
+          python -m unittest discover -s tests -p test_quantification.py -v
+          python -m unittest discover -s tests -p test_dia_reuse.py -v
+          python -m unittest discover -s tests -p test_matrix_catalog.py -v
+
+  python_distribution:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Build and audit both distributions
+        run: |
+          python -m pip install build twine
+          python -m build
+          python -m twine check dist/*
+          python scripts/validate_distribution.py
+      - name: Install the wheel and R statistics
+        run: |
+          python -m pip install dist/*.whl
+          sudo apt-get update
+          sudo apt-get install -y r-base r-bioc-limma r-bioc-edger r-cran-jsonlite
+      - name: Test installed commands, verified reuse, and damaged-output recovery
+        env:
+          FUN_PROTEOMICS_TEST_INSTALLED: '1'
+          PROTEOMICS_RSCRIPT: /usr/bin/Rscript
+        run: |
+          python -m unittest discover -s tests -p test_package_cli.py -v
+          python tests/run_package_smoke.py

fun_proteomics-0.5.0/.gitignore

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+# Local study configuration and data
+/config.local.json
+*.local.json
+*.local.config
+/ui_configs/
+/inputs/
+/data/
+*.d/
+*.raw
+*.RAW
+*.mzML
+*.mzXML
+*.wiff
+*.wiff2
+*.tdf
+*.tdf_bin
+*.fasta
+*.fa
+*.fastq*
+# Generated results, caches, and installed modules
+/results*/
+/final_results*/
+/analysis_details/
+/work*/
+/logs/
+/.nextflow*
+/.runtime/
+/.test-runtime*/
+/.bootstrap/
+/.database_cache/
+/modules/*
+!/modules/diapasef/
+/provenance/
+/reference_results/
+__pycache__/
+*.pyc
+.venv*/
+# Registered software, archives and credentials
+/software/
+*.jar
+*.zip
+*.tar.gz
+.env
+.env.*
+*registration*
+*license_key*
+*.pem
+*.key
+
+/zscore/
+/VALIDATION_COMPLETE.txt
+
+# Local caches, backups, preparation and study artifacts
+/cache/
+/configs/
+/.migration_backup/
+/.ipynb_checkpoints/
+*.ipynb
+*.log
+*.log.*
+*.pid
+*.parquet
+*.speclib
+*.mzBIN*
+*.quant
+
+# Imported provider tables and review artifacts stay local
+/service_quantification/
+/imports/
+/benchmarks/
+/validation/
+/*.csv
+/*.tsv
+/*.xlsx
+
+# Python distributions and launcher state
+/build/
+/dist/
+*.egg-info/
+.fun_proteomics/
+/src/fun_proteomics/_workflow/

fun_proteomics-0.5.0/GITHUB_UPLOAD.md

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+# GitHub preparation
+
+The public repository is **cfarkas/fun_proteomics**. The source package supports native
+Bruker DDA-PASEF through FragPipe and DIA-PASEF through DIA-NN, using the same
+`main.nf` entry point. `nextflow run main.nf --interactively` configures either
+acquisition type. Direct DIA runs use `nextflow run main.nf --dia_config study.json`;
+the browser generates that native DIA configuration while preserving the editable study.
+
+## Validate and package
+
+From the repository directory, after installing the runtime described in README:
+
+```bash
+.runtime/env/bin/python scripts/validate_repo.py
+bash tests/run_all.sh
+bash tests/run_smoke.sh
+python3.12 tests/run_diapasef_smoke.py
+python3 scripts/package_source.py
+```
+
+Packaging creates `../pasef-proteomics-source.zip`, its `.sha256` checksum and `SOURCE_SHA256SUMS`. It
+uses an explicit source allowlist and excludes symlinks, local configurations,
+results, runtime environments, input data and installed search engines. Only
+the source-controlled DIA module is included from `modules/`.
+
+The GitHub Actions workflow runs source checks, unit tests and DDA/DIA synthetic
+execution/resume checks. Synthetic checks produce no scientific measurements.
+Real searches require user-supplied acquisitions, FASTA and separately obtained
+search engines.
+
+## Upload the source repository
+
+Use the public GitHub repository `cfarkas/fun_proteomics`. If Git has already been initialized and a source commit prepared,
+start with the remote command below. Otherwise initialize a source-only extracted
+archive with `git init -b main`, review `git status --short`, add the source files
+and commit them.
+
+For a clean source-only checkout:
+
+```bash
+git remote add origin git@github.com:cfarkas/fun_proteomics.git
+git push -u origin main
+```
+
+No remote repository is created and nothing is uploaded by the local preparation
+or packaging commands. The archive also supports GitHub's file-upload interface
+after extraction.
+
+## What stays local
+
+Keep native acquisitions, study/sample identifiers, FASTA databases, reference
+matrices, downloaded or registered tools, licenses/registration credentials,
+local configuration JSON, browser drafts and UI state, generated `ui_configs/dia/`
+inputs, logs, cached work and results outside Git. Use the
+templates under `examples/` for public configuration examples.
+
+Original source and documentation use the [MIT license](LICENSE). Separately installed tools retain their own licenses; see [LICENSE_NOTES.md](LICENSE_NOTES.md).
+
+## Clean installation location
+
+Extract the source ZIP into the parent directory where you want the repository.
+For example, `unzip pasef-proteomics-source.zip -d /path/to/projects` creates
+`/path/to/projects/pasef-proteomics`. Use a new destination so existing files are preserved.
+The package is small because it excludes raw data, outputs, work caches and runtimes.
+Choose an output directory outside the source repository for each real study.
+
+Version 0.4.0 adds a top-level matrix catalogue, annotated DIA protein/gene intensities,
+all-pairs intensity comparisons, post-search count reanalysis and service detection
+benchmarks. The separate DIA CI job exercises actual reporting/statistical code on
+synthetic precursor tables; spectrum searches in CI remain explicitly stubbed.
+
+## Python distribution
+
+The public package name is `fun_proteomics` (PyPI normalizes it to `fun-proteomics`). The repository is `cfarkas/fun_proteomics`; the license is MIT. Build and inspect both distributions before publishing:
+
+```bash
+python -m build
+python -m twine check dist/*
+```
+
+The wheel contains a checked workflow source bundle. Both source distribution and wheel exclude local acquisitions, results, tools and credentials. Tests install the wheel outside the checkout and exercise native Python reporting and folder continuation. Publishing to PyPI requires an authorized account or a configured trusted publisher. A release workflow is provided for the `pypi` GitHub environment.

fun_proteomics-0.5.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 cfarkas and fun_proteomics contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

fun_proteomics-0.5.0/LICENSE_NOTES.md

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+# Licensing and redistribution
+
+The original workflow code and documentation are distributed under the MIT license in LICENSE. Copyright (c) 2026 cfarkas and fun_proteomics contributors. Third-party tools retain their own licenses; the MIT license does not relicense them.
+
+FragPipe, MSFragger, IonQuant, diaTracer, DIA-NN, Nextflow and the Python/R dependencies retain their own licenses and citation requirements. Obtain registered software through the official distribution links in assets/tool_versions.json. Their binaries, vendor SDKs, private URLs, registration details and keys are not included.
+
+This source package contains no experimental acquisitions or study results. The FragPipe settings file is a configuration, not a bundled copy of the application. No files have been published by preparing this package.

fun_proteomics-0.5.0/MANIFEST.in

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+include pyproject.toml MANIFEST.in PACKAGE_README.md README.md OUTPUTS.md GITHUB_UPLOAD.md LICENSE LICENSE_NOTES.md SOURCE_SHA256SUMS main.nf nextflow.config setup_environment.sh .gitignore .gitattributes
+recursive-include src/fun_proteomics *.py
+recursive-include assets *.html *.json *.txt *.workflow
+recursive-include pipeline_lib *.py *.R
+recursive-include scripts *.py *.sh
+recursive-include tests *.py *.sh
+recursive-include envs *.yml
+recursive-include examples *.json *.csv *.tsv *.md
+recursive-include modules/diapasef *.py *.nf *.toml *.txt *.md
+recursive-include .github *.yml
+prune src/fun_proteomics/_workflow
+prune .runtime
+prune .test-runtime
+prune results
+prune validation
+global-exclude *.pyc *.local.json *.local.config .DS_Store

fun_proteomics-0.5.0/OUTPUTS.md

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+# Results directory
+
+## Matrix entry point and DIA outputs
+
+Every delivered matrix is available in both **CSV and TSV**, with identical identifiers, values and missing cells. `MATRICES.html` has separate links for both formats; the index is also supplied as `MATRICES.csv` and `MATRICES.tsv`.
+
+Start with `final_results/MATRICES.html` or its machine-readable `MATRICES.csv`.
+For DDA, `matrices/<cohort>/<dda|ddaplus>/protein_counts.csv` is a checksum-verified copy
+of the existing annotated raw count matrix. Peptide and selected gene matrices are beside it.
+The historical detailed folders remain available. `python pipeline_lib/matrix_catalog.py /data/run/final_results`
+adds this index to completed results without statistical refitting.
+
+For DIA, `matrices/<sample_type>/protein_intensities.csv` contains `Protein.Group`, `Genes`,
+protein names, gene mapping status/source and sample intensities. `gene_intensities.csv` sums quantities
+only for unambiguous single-gene groups, with missingness retained and no duplication of ambiguous groups.
+These are protein-derived gene rollups, not RNA counts or independently tested gene identification FDR.
+Unmapped/ambiguous/partial assignments are listed under `quality_control/<sample_type>/`.
+
+DIA comparisons use `differential_expression/<sample_type>/<protein|gene>/<reference>_vs_<comparison>/`.
+`all_results.csv` retains insufficient-observation rows; `significant_results.csv` uses the selected BH cutoff.
+Positive logFC means comparison minus reference. `results_index.csv`, model settings, log2 matrices,
+normalization offsets, design and R session document each analysis. Every contrast and feature level has
+its own FDR family. No imputation or subject/batch adjustment is inferred.
+
+`benchmark/<sample_type>/detection_summary.csv` reports pipeline/service totals, shared, pipeline-only,
+service-only, net difference and percentage change for each matched sample and the union. `protein_membership.csv`
+lists each category. Zero baseline produces a blank percentage. Exact canonical group membership is required;
+protein groups are never expanded into independent proteins. Search/grouping/FDR differences limit interpretation.
+Native DIA evidence is under `analysis_details/`; raw acquisition files are never copied into deliverables.
+
+
+Open **`<outdir>/final_results/START_HERE.html`**. The dashboard works offline and separates the study overview, main results, optional analyses, counts/QC and interpretation guidance. Statistical tables can be filtered by analysis, search mode, method and result status. Each test links to its full results and significant subset.
+
+```text
+<outdir>/
+├── final_results/
+│   ├── START_HERE.html
+│   ├── README.md
+│   ├── results_index.csv
+│   ├── FINAL_RESULTS_COMPLETE
+│   ├── main_results/
+│   │   ├── differential_expression/<cohort>/<dda|ddaplus>/<comparison>/<feature_type>/
+│   │   │   ├── <method>_all_results.csv
+│   │   │   └── <method>_significant_results.csv
+│   │   ├── counts/<cohort>/<dda|ddaplus>/
+│   │   │   ├── raw/*_counts.csv
+│   │   │   ├── normalized/*_normalized_cpm.csv
+│   │   │   ├── normalized/*_log2_cpm.csv
+│   │   │   └── zscore/*_zscore.csv
+│   │   └── quality_control/
+│   │       ├── sample_annotations.csv
+│   │       ├── analysis_summary.csv
+│   │       ├── comparisons.csv
+│   │       └── condition_columns.csv
+│   └── optional_analyses/
+│       ├── gene_counts/{counts,comparisons}/  # optional gene and gene-modification results
+│       ├── statistics/
+│       │   ├── comparisons/<cohort>/<mode>/<comparison>/<peptide|isoform>/
+│       │   │   ├── <method>_all_results.csv
+│       │   │   └── <method>_significant_results.csv
+│       │   └── counts/<cohort>/<mode>/<raw|matrices|zscore>/
+│       ├── drug_interaction/<cohort>/<mode>/<protein|gene|peptide>/
+│       │   ├── <method>_all_results.csv
+│       │   └── <method>_significant_results.csv
+│       ├── peptide_isoforms/<cohort>/<mode>/
+│       │   ├── peptide_evidence.csv
+│       │   ├── peptide_condition_summary.csv
+│       │   └── isoform_evidence.csv
+│       └── immunopeptidomics/<cohort>/dda/
+│           ├── peptides.csv
+│           ├── sample_summary.csv
+│           ├── length_distribution.csv
+│           └── binding_input.txt
+├── analysis_details/
+│   ├── <cohort>/<dda|ddaplus>/run/         # original search files
+│   ├── <cohort>/<dda|ddaplus>/tables_*/    # detailed search counts
+│   ├── reporting/<cohort>/<mode>/         # main model inputs, filters, assignments
+│   ├── reporting/result_audit/           # settings, optional model diagnostics, file checksums
+│   └── final/                           # search summary and workbook
+├── logs/
+└── database/search.fasta
+```
+
+Only generated analyses have result folders. Existing search-level coverage tables are included under `main_results/quality_control/` when available. `method_notes.csv` is present when a method cannot be estimated. The overall condition test uses `overall_condition_test/` in place of a named comparison. Methods stay together under the biological comparison, while cohorts and DDA/DDA+ remain separate.
+
+`results_index.csv` records section, analysis, cohort, mode, evidence type, method, test type, comparison, reported/tested/significant feature counts, status, FDR cutoff and both result paths. It describes separate statistical families; it is not a merged list of discoveries. Dashboard totals count tables, not unique significant features across methods.
+
+## Main analyses
+
+Protein differential abundance is primary; supporting peptide and selected protein-modification comparisons follow. Gene-level results appear only under Optional analyses.
+
+**Counts.** Protein and peptide matrices contain spectral counts. Gene counts sum peptide spectral counts only for unambiguous gene assignments, using Gene plus Mapped Genes. Gene results describe proteomics-derived evidence, not RNA expression. Modification-by-gene and modification-by-protein matrices count distinct modified peptide sequences per entity and modification type: repeated spectra, charges and sites do not multiply a sequence within one type. A peptide with two modification types can contribute once to each type. Ambiguous gene/protein assignments are excluded and audited. Supporting `modification_counts.csv` contains peptidoform PSM counts instead.
+
+**Comparisons.** Positive pairwise `logFC` means comparison minus reference. Overall tests ask whether any condition differs and have no single fold-change direction. `PValue` is unadjusted; `FDR` is the Benjamini–Hochberg adjusted p-value within each method, feature type, contrast, cohort and search mode. Do not select the smallest p-value across methods as a combined test. Condition means and detection counts are descriptive; use the named comparisons to assess differences.
+
+**Normalization and low counts.** Standard counts use TMM. Sparse modification tests use TMMwsp and edgeR's small-count quasi-likelihood GLM (`legacy=FALSE`, robust moderation); edgeRun and limma-voom are complementary methods. Filtering is optional, with saved thresholds in the model records. No imputation or pseudocounts are added to the count-model inputs. Modification counts do not measure occupancy, localization-filtered sites or protein-adjusted modification changes.
+
+**Matrices.** Counts are grouped by cohort and search mode rather than combined into a matrix with blank columns from other cohorts. Normalization is separate for each evidence type. Z-scores standardize rows of log2 CPM; constant rows are zero and empty libraries are missing. They are visualization values, not statistical tests. DDA and DDA+ must not be summed or treated as biological replicates. Independent replication and comparable sampling are assumed; batch and subject effects are not inferred.
+
+## Optional analyses
+
+**Gene counts and comparisons.** Select `optional_analyses.gene_counts=true` in Optional analyses → Gene counts. `gene_counts/counts/<cohort>/<mode>/` contains raw, normalized and z-score matrices; `gene_counts/comparisons/` contains named condition and overall tests, including selected gene-modification tests. These use the DEPs methods, reference condition, FDR and count filters; testing requires DEPs enabled. Shared-gene peptides are excluded from this aggregate only. Protein counts and their separately corrected statistics are unaffected. The same Gene counts option includes gene-level drug-interaction tests when that analysis is enabled; those tests use its own methods and FDR. Existing studies preserve gene analyses; new studies default off.
+
+**Peptide and isoform evidence.** Peptides are remapped against all searched FASTA targets, with I/L indistinguishable. Shared sequences remain ambiguous. Isoform specificity requires a uniquely matching accession with alternative isoforms in the searched FASTA. The evidence tables include coverage, detection by condition and unique-peptide counts; they do not establish full proteoforms or isoform-identification FDR.
+
+**Statistical comparisons.** Selected peptide spectral counts and isoform-discriminating counts are compared with their own methods, reference/all-pairs design, FDR and filtering settings. edgeR's small-count model and optional limma-voom use TMMwsp, retaining full-library offsets through filtering. Canonical-only or ambiguous isoform assignments are excluded with reasons in the audit directory. The FDR concerns condition differences; it does not establish isoform identity or switching.
+
+**Drug interaction.** `interaction_log2FC` is combination minus drug A minus drug B plus control on a log2 scale. The null is multiplicative on the original abundance scale. Its sign describes proteomic nonadditivity, not beneficial synergy. Tables record `dose_time_matching_confirmed` and `analysis_interpretation`; unconfirmed matching is an exploratory combination contrast. This annotation does not change the test. Methods have separate results and FDR: edgeR quasi-likelihood, limma-voom, and/or negative-binomial Monte Carlo simulation.
+
+Limma interaction tables include moderated t-statistics and 95% effect confidence intervals. Monte Carlo tables include the likelihood-ratio statistic, empirical p-value, FDR, exceedance/valid simulation counts, seed, minimum p-value, simulation standard error and exact binomial interval for the conditional tail probability. Dispersion and normalization stay fixed during simulation, so calibration is approximate. Its interval describes simulation uncertainty, not biological effect uncertainty. The p-value floor `1/(simulations+1)` can limit BH discoveries. Voom weights, null fits, designs, offsets and simulation settings are supporting model records under `analysis_details/reporting/result_audit/drug_interaction/`.
+
+**HLA-enriched samples.** Dedicated reports contain peptide evidence, sample summaries, lengths and stripped sequences for external binding prediction. Identification applies 1% PSM FDR without a 1% peptide/protein FDR claim; this is separate from differential-test FDR. MBR is off. Differential tests use peptide counts; supporting gene/protein annotations do not measure source-protein abundance. No binding predictor or allele assignment is run.
+
+## Status and provenance
+
+**No significant results** means tests ran and no features passed FDR. **Insufficient evidence** means tests could not be estimated. **No eligible evidence** means there are no eligible rows. Full tables preserve reported nonsignificant/untestable features; untestable rows have blank p-values/FDR and an explicit status. Empty significant subsets are valid and remain downloadable. Counts excluded from main fits remain in count matrices and filter reports.
+
+Final result tables are copied without changing statistics. `--continue` reuses this study’s matching completed Nextflow tasks and verified completed FragPipe searches; preserve `work/`, `.nextflow/` and the output directory. Search checkpoints and provenance remain with completed search files. `analysis_details/reporting/result_audit/file_manifest.csv` records source/destination paths and verified SHA-256 hashes. The audit directory holds run settings, R session details, model inputs, exclusion/filter reports and normalization factors. Historical indices/settings there describe the original computation; use the final `results_index.csv` for current result locations.
+
+Open-search discovery is no longer part of the pipeline or final results. Older configurations drop that option and mass-shift comparisons on loading. An existing completed run can be reformatted without searching or fitting models:
+
+```bash
+.runtime/env/bin/python pipeline_lib/result_layout.py /path/to/output/final_results --preserve-original
+```
+
+The prior layout, including retired discovery results, is preserved under `analysis_details/previous_result_layout_*`. Future runs generate the same curated final layout automatically.

fun_proteomics-0.5.0/PACKAGE_README.md

@@ -0,0 +1,61 @@
+# fun_proteomics
+
+Portable Python and Nextflow launchers for DDA-PASEF and DIA-PASEF proteomics. MIT licensed, maintained by [cfarkas](https://github.com/cfarkas).
+
+```bash
+python -m pip install fun_proteomics
+fun_proteomics --help
+```
+
+Python 3.11 or newer is required. Linux is the supported execution platform. Native DIA spectrum searches use their separately pinned Python 3.12 environment. The Python package includes the workflow source, analysis/reporting code and examples; raw acquisitions, study results and registered search binaries are excluded.
+
+## Continue a folder from anywhere
+
+```bash
+fun_proteomics --continue /data/my_study
+# Equivalent native Python entry point:
+python -m fun_proteomics --continue /data/my_study
+```
+
+The folder may be a run root or its `final_results/` directory. The launcher detects its saved state and reusable DIA searches. Completed native deliveries are checked against their output checksums and recorded inputs; valid results are reused. An incomplete or damaged native delivery is rebuilt from its verified inputs or completed searches into `continuations/<timestamp>/`, preserving earlier attempts. Nextflow-managed runs use their recorded session and work cache. Changed raw acquisitions fail reuse when a recorded checksum baseline exists. `--hash-raw` requests a full raw-file hash check; otherwise recorded sizes/timestamps are checked and changed files are hashed. A legacy run without historical raw hashes receives a new baseline, not a claim of retrospective raw identity.
+
+```bash
+fun_proteomics --continue /data/old_run --outdir /data/new_delivery \
+  --service-matrix tissue=/data/service.tsv --independent-samples --hash-raw
+```
+
+Use `--independent-samples` only when each row represents a different biological sample. This preserves old replicate labels and uses unique sample IDs for modeling. The native DIA reporting path runs all unordered condition pairs at protein and unambiguous gene level, using limma-trend on log2 positive intensities without imputation. CSV and TSV matrices, results, service detection gains/losses, quality control and provenance have separate folders.
+
+## Start a raw-data workflow
+
+```bash
+fun_proteomics run --config /data/dda.json --outdir /data/results
+fun_proteomics run --dia-config /data/dia.json --outdir /data/results_dia
+fun_proteomics ui
+```
+
+These commands invoke Nextflow. Java and Nextflow are required; registered spectrum-search programs remain separate installations with their own licenses. Use `fun_proteomics doctor` to inspect dependencies, or `--project /path/to/checkout` to reuse an existing checkout and its runtime. Packaged workflow files are verified and extracted to a writable user cache; `--cache-dir` changes that location.
+
+Direct Nextflow remains supported:
+
+```bash
+nextflow run "$(fun_proteomics workflow-path)/main.nf" --continue /data/my_study
+```
+
+Native matrix analysis is available without Nextflow:
+
+```bash
+fun_proteomics quantify --matrix /data/proteins.tsv --samples /data/samples.csv \
+  --outdir /data/quantification --differential
+```
+
+The installed `quantify` command writes its organized delivery to `OUTDIR/final_results/` and stores its continuation state in `OUTDIR/.fun_proteomics/`. Use the same `--continue OUTDIR` command for matrix analyses.
+
+Differential analysis also requires R with `limma` and `jsonlite`; DDA count modeling requires the corresponding Bioconductor packages. Configure existing installations using `--rscript` and `--r-library` before the subcommand. R and registered search engines are not installed by pip.
+
+```bash
+fun_proteomics --rscript /usr/bin/Rscript --r-library /data/R-library \
+  --continue /data/my_study
+```
+
+Read the full workflow documentation at [github.com/cfarkas/fun_proteomics](https://github.com/cfarkas/fun_proteomics). More detected protein groups do not alone demonstrate better accuracy: service searches may use different databases, grouping and confidence settings.

fun_proteomics-0.5.0/PKG-INFO

@@ -0,0 +1,94 @@
+Metadata-Version: 2.4
+Name: fun_proteomics
+Version: 0.5.0
+Summary: Portable PASEF proteomics workflows, verified continuation, and protein/gene differential analysis
+Author: cfarkas
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/cfarkas/fun_proteomics
+Project-URL: Repository, https://github.com/cfarkas/fun_proteomics
+Project-URL: Issues, https://github.com/cfarkas/fun_proteomics/issues
+Keywords: proteomics,PASEF,DIA,Nextflow,differential-abundance
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: LICENSE_NOTES.md
+License-File: modules/diapasef/NOTICE.md
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: pandas<3,>=2.2
+Requires-Dist: matplotlib<4,>=3.8
+Requires-Dist: pyarrow<26,>=19
+Requires-Dist: openpyxl<4,>=3.1
+Requires-Dist: jsonschema<5,>=4.23
+Provides-Extra: build
+Requires-Dist: build>=1.2; extra == "build"
+Requires-Dist: twine>=6; extra == "build"
+Dynamic: license-file
+
+# fun_proteomics
+
+Portable Python and Nextflow launchers for DDA-PASEF and DIA-PASEF proteomics. MIT licensed, maintained by [cfarkas](https://github.com/cfarkas).
+
+```bash
+python -m pip install fun_proteomics
+fun_proteomics --help
+```
+
+Python 3.11 or newer is required. Linux is the supported execution platform. Native DIA spectrum searches use their separately pinned Python 3.12 environment. The Python package includes the workflow source, analysis/reporting code and examples; raw acquisitions, study results and registered search binaries are excluded.
+
+## Continue a folder from anywhere
+
+```bash
+fun_proteomics --continue /data/my_study
+# Equivalent native Python entry point:
+python -m fun_proteomics --continue /data/my_study
+```
+
+The folder may be a run root or its `final_results/` directory. The launcher detects its saved state and reusable DIA searches. Completed native deliveries are checked against their output checksums and recorded inputs; valid results are reused. An incomplete or damaged native delivery is rebuilt from its verified inputs or completed searches into `continuations/<timestamp>/`, preserving earlier attempts. Nextflow-managed runs use their recorded session and work cache. Changed raw acquisitions fail reuse when a recorded checksum baseline exists. `--hash-raw` requests a full raw-file hash check; otherwise recorded sizes/timestamps are checked and changed files are hashed. A legacy run without historical raw hashes receives a new baseline, not a claim of retrospective raw identity.
+
+```bash
+fun_proteomics --continue /data/old_run --outdir /data/new_delivery \
+  --service-matrix tissue=/data/service.tsv --independent-samples --hash-raw
+```
+
+Use `--independent-samples` only when each row represents a different biological sample. This preserves old replicate labels and uses unique sample IDs for modeling. The native DIA reporting path runs all unordered condition pairs at protein and unambiguous gene level, using limma-trend on log2 positive intensities without imputation. CSV and TSV matrices, results, service detection gains/losses, quality control and provenance have separate folders.
+
+## Start a raw-data workflow
+
+```bash
+fun_proteomics run --config /data/dda.json --outdir /data/results
+fun_proteomics run --dia-config /data/dia.json --outdir /data/results_dia
+fun_proteomics ui
+```
+
+These commands invoke Nextflow. Java and Nextflow are required; registered spectrum-search programs remain separate installations with their own licenses. Use `fun_proteomics doctor` to inspect dependencies, or `--project /path/to/checkout` to reuse an existing checkout and its runtime. Packaged workflow files are verified and extracted to a writable user cache; `--cache-dir` changes that location.
+
+Direct Nextflow remains supported:
+
+```bash
+nextflow run "$(fun_proteomics workflow-path)/main.nf" --continue /data/my_study
+```
+
+Native matrix analysis is available without Nextflow:
+
+```bash
+fun_proteomics quantify --matrix /data/proteins.tsv --samples /data/samples.csv \
+  --outdir /data/quantification --differential
+```
+
+The installed `quantify` command writes its organized delivery to `OUTDIR/final_results/` and stores its continuation state in `OUTDIR/.fun_proteomics/`. Use the same `--continue OUTDIR` command for matrix analyses.
+
+Differential analysis also requires R with `limma` and `jsonlite`; DDA count modeling requires the corresponding Bioconductor packages. Configure existing installations using `--rscript` and `--r-library` before the subcommand. R and registered search engines are not installed by pip.
+
+```bash
+fun_proteomics --rscript /usr/bin/Rscript --r-library /data/R-library \
+  --continue /data/my_study
+```
+
+Read the full workflow documentation at [github.com/cfarkas/fun_proteomics](https://github.com/cfarkas/fun_proteomics). More detected protein groups do not alone demonstrate better accuracy: service searches may use different databases, grouping and confidence settings.