gfviewer 2.0.0__tar.gz

gfviewer-2.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Sakshar Chakravarty and Stefano Lonardi
+
+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.

gfviewer-2.0.0/MANIFEST.in

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+# Files to ship in the source distribution (sdist) built by `python -m build`.
+# The wheel contents are controlled by [tool.setuptools] in pyproject.toml.
+
+include README.md
+include LICENSE
+include requirements.txt
+include environment.yml
+include pyproject.toml
+
+recursive-include docs *.md
+recursive-include gfviewer *.py
+recursive-include gfviewer_web *.py
+
+# Web portal assets (only used when running the portal from a source checkout).
+recursive-include templates *.html
+recursive-include static *.css *.js *.png *.svg
+
+# Tests and the fixture builder.
+include flaskapp.py gfviewer.py
+recursive-include tests *.py
+include tests/*.csv tests/*.txt
+
+# Never ship generated output or large bundled datasets.
+prune static/output
+prune static/tests
+prune uploads
+prune instance
+global-exclude __pycache__ *.py[cod] .DS_Store

gfviewer-2.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: gfviewer
+Version: 2.0.0
+Summary: Visualize and quantify the localization of multigene families across chromosomes
+Author: Sakshar Chakravarty, Stefano Lonardi
+Maintainer-email: Stefano Lonardi <stelo@ucr.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/sakshar/GFViewer
+Project-URL: Repository, https://github.com/sakshar/GFViewer
+Project-URL: Documentation, https://github.com/sakshar/GFViewer/blob/main/docs/INSTALL.md
+Project-URL: Issues, https://github.com/sakshar/GFViewer/issues
+Keywords: bioinformatics,genomics,multigene family,gene family,chromosome,ideogram,karyotype,visualization,comparative genomics,localization,Ripley K
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Environment :: Web Environment
+Classifier: Framework :: Flask
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+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
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython>=1.80
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: pandas>=1.5
+Requires-Dist: numpy>=1.22
+Requires-Dist: openpyxl>=3.0
+Requires-Dist: Pillow>=9.0
+Requires-Dist: reportlab>=3.6
+Requires-Dist: PyPDF2>=3.0
+Requires-Dist: PyYAML>=6.0
+Provides-Extra: web
+Requires-Dist: Flask>=2.2; extra == "web"
+Requires-Dist: Werkzeug>=2.2; extra == "web"
+Requires-Dist: gunicorn>=21.0; extra == "web"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Provides-Extra: build
+Requires-Dist: build>=1.0; extra == "build"
+Requires-Dist: twine>=4.0; extra == "build"
+
+# GFViewer
+
+Visualize the localization of **multigene families** across the chromosomes of a
+genome, and quantify how those families are distributed.
+
+GFViewer draws round-capped chromosome ideograms with each family in its own
+colour (``+`` strand above the axis, ``-`` below), optionally marks centromeres,
+and can compute localization statistics. Output is fully vector and can be saved
+as **PDF, SVG, PNG, JPG, TIFF or EPS**.
+
+Version 2 rewrites the rendering engine on top of matplotlib (the old
+BioPython/`BasicChromosome` engine is kept at `gfviewer.legacy` for one
+release), removes the 19-family ceiling, adds BED / GFF3 / GTF input, a style
+system, an analytics module, and an interactive web portal.
+
+## Install
+
+```bash
+pip install gfviewer                      # the `gfviewer` command-line tool
+```
+
+From a source checkout (development, tests, or the web portal):
+
+```bash
+conda env create -f environment.yml      # or: python -m venv .venv && source .venv/bin/activate
+conda activate gfviewer
+pip install -e ".[web,dev]"               # editable, with Flask + pytest
+```
+
+A full pip-installation and command-line walkthrough — isolated environments,
+every flag with worked examples, troubleshooting — is in
+[`docs/INSTALL.md`](docs/INSTALL.md), and is mirrored on the web portal's
+**Install** page. Build distributable artifacts with `scripts/build_wheel.sh`.
+
+## Command line
+
+```bash
+gfviewer -d genes.tsv -g genome.fasta -o out/ \
+         -f pdf svg png --analytics -cen \
+         --tick-style lollipop --title "My organism"
+```
+
+Key options (`gfviewer --help` for the full list):
+
+| Flag | Meaning |
+|------|---------|
+| `-d/--data` | one or more annotation files (`.xlsx/.csv/.tsv/.bed/.gff3/.gtf`) |
+| `-g/--genome` | FASTA, `.fai`, `chrom.sizes`, or `chrom,length` table |
+| `-c/--colors` | colour-map file (`family,index` / `family,#hex` / `family,r,g,b`) |
+| `-m/--mapping` | `gene_id,gene_family` map (single BED/GFF input) |
+| `--family-attr` | GFF3/GTF attribute that holds the family |
+| `-f/--format` | export formats |
+| `--collapse-rare` | fold infrequent families into "Other" above the 40-family cap |
+| `--style` / `--save-style` | load / write a YAML/JSON style file |
+| `--analytics` | also write per-family statistics as CSV/JSON |
+| `--no-titles` | omit titles from the exported figure and analytics-chart images |
+| `-cen` | draw centromeres |
+
+### Input formats
+
+* **Table** — columns `gene_id, gene_family, chromosome, start, end, strand`
+  (1-based, inclusive; header synonyms accepted). A `centromere` value in
+  `gene_family` (strand `0`) marks a centromere.
+* **BED** — 0-based half-open, converted automatically. One file → column 4 is
+  the family; several files → each file's base name is the family; one file plus
+  a mapping file → family from the map.
+* **GFF3 / GTF** — 1-based; gene-like feature types kept; family taken from
+  `--family-attr` (default search: `gene_family`, `Family`, `gene_biotype`,
+  `Name`, …).
+
+### Analytics
+
+`--analytics` writes `analytics_*.csv` / `.bed`, `analytics_summary.json` and
+four figures (`analytics_genes_per_family`, `analytics_positional_profile`,
+`analytics_ripley`, `analytics_family_proximity` — one per requested figure
+format). It computes:
+
+* per-family counts split into genes on chromosomes vs. unplaced/stray contigs,
+  linear density, gene length, strand fraction;
+* permutation tests for **telomere-** and (with a centromere track)
+  **centromere-proximal** bias, plus **p-arm / q-arm** occupancy;
+* **tandem-array** detection and a **tandem / proximal / dispersed** duplication
+  mode per family;
+* **multi-scale clustering** — edge-corrected 1-D **Ripley's K/L** with a
+  permutation envelope (`--ripley-scales`);
+* **chromosome-enrichment** (binomial, per family × chromosome), **strand bias**,
+  and per-chromosome **family diversity** (Shannon / evenness);
+* a binned **positional density profile** ("metachromosome" plot);
+* a **family × family proximity matrix** with average-linkage clustering;
+* **multigene-family hotspots** — a Poisson window scan, merged and written as a
+  table and a **BED** file (`--hotspot-window`);
+* optional pairwise **co-localization** (`--colocalization`).
+
+Every per-family / per-pair / per-window test carries a Benjamini–Hochberg
+`q_value`. See `templates/help.html` (the *Downloadable outputs* section) for the
+column-by-column layout of each file.
+
+## Web portal
+
+```bash
+# development
+python flaskapp.py                       # http://localhost:5001
+
+# production
+gunicorn -w 1 --threads 4 -b 0.0.0.0:5001 "gfviewer_web:create_app()"
+```
+
+Uploads are rendered on a background thread pool behind an async job API
+(`POST /api/jobs` → `GET /api/jobs/<id>/status` → results page). The results page
+embeds the SVG with an editor for choosing which families and chromosomes to
+draw, recolouring, moving the legend and labels, changing fonts and mark style,
+toggling whether titles are baked into the image files, then re-rendering and
+exporting. Analytics figures are shown inline, and two buttons download
+**everything as a ZIP** — either as produced, or re-rendered in every figure
+format. `GET /api/health` is a readiness probe.
+
+**Usage monitor.** A privacy-respecting counter (`/stats`, or JSON at
+`/api/stats`) tracks page views, unique visitors per day (a salted daily hash —
+no IPs, cookies or other personal data are stored), jobs submitted / completed /
+failed, example-dataset runs and downloads, with a rolling ~120-day daily
+series. Counters persist to `instance/usage.json`.
+
+Configuration (environment variables): `GFVIEWER_DATA_DIR`,
+`GFVIEWER_MAX_UPLOAD_MB` (25), `GFVIEWER_WORKERS` (2), `GFVIEWER_JOB_TTL_HOURS`
+(24), `GFVIEWER_USAGE_FILE`, `GFVIEWER_STATS_TOKEN` (require `?token=` on
+`/stats`), `SECRET_KEY`, `PORT`.
+
+## Example datasets
+
+`python tests/make_fixtures.py` builds every bundled dataset into
+`static/tests/`: the three *Babesia* sets, the 6-family set re-expressed in
+every input format (`formats/` — BED, per-family BED, BED + mapping, GFF3, GTF),
+and two synthetic sets — 10 random gene families on the *Arabidopsis* (TAIR10)
+chromosomes and 20 on *C. elegans* (WBcel235). The web home page lists them all
+with **Run** (submits the job) and **Download** buttons, plus *Download every
+dataset (ZIP)*.
+
+## Tests
+
+```bash
+python tests/make_fixtures.py            # once, to build the example datasets
+pytest -q
+```
+
+## Citation
+
+Chakravarty S. & Lonardi S. *Visualizing the localization of multigene families
+with GFViewer.* Development supported by NIH grant 1-R01-AI169543-01.

gfviewer-2.0.0/README.md

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+# GFViewer
+
+Visualize the localization of **multigene families** across the chromosomes of a
+genome, and quantify how those families are distributed.
+
+GFViewer draws round-capped chromosome ideograms with each family in its own
+colour (``+`` strand above the axis, ``-`` below), optionally marks centromeres,
+and can compute localization statistics. Output is fully vector and can be saved
+as **PDF, SVG, PNG, JPG, TIFF or EPS**.
+
+Version 2 rewrites the rendering engine on top of matplotlib (the old
+BioPython/`BasicChromosome` engine is kept at `gfviewer.legacy` for one
+release), removes the 19-family ceiling, adds BED / GFF3 / GTF input, a style
+system, an analytics module, and an interactive web portal.
+
+## Install
+
+```bash
+pip install gfviewer                      # the `gfviewer` command-line tool
+```
+
+From a source checkout (development, tests, or the web portal):
+
+```bash
+conda env create -f environment.yml      # or: python -m venv .venv && source .venv/bin/activate
+conda activate gfviewer
+pip install -e ".[web,dev]"               # editable, with Flask + pytest
+```
+
+A full pip-installation and command-line walkthrough — isolated environments,
+every flag with worked examples, troubleshooting — is in
+[`docs/INSTALL.md`](docs/INSTALL.md), and is mirrored on the web portal's
+**Install** page. Build distributable artifacts with `scripts/build_wheel.sh`.
+
+## Command line
+
+```bash
+gfviewer -d genes.tsv -g genome.fasta -o out/ \
+         -f pdf svg png --analytics -cen \
+         --tick-style lollipop --title "My organism"
+```
+
+Key options (`gfviewer --help` for the full list):
+
+| Flag | Meaning |
+|------|---------|
+| `-d/--data` | one or more annotation files (`.xlsx/.csv/.tsv/.bed/.gff3/.gtf`) |
+| `-g/--genome` | FASTA, `.fai`, `chrom.sizes`, or `chrom,length` table |
+| `-c/--colors` | colour-map file (`family,index` / `family,#hex` / `family,r,g,b`) |
+| `-m/--mapping` | `gene_id,gene_family` map (single BED/GFF input) |
+| `--family-attr` | GFF3/GTF attribute that holds the family |
+| `-f/--format` | export formats |
+| `--collapse-rare` | fold infrequent families into "Other" above the 40-family cap |
+| `--style` / `--save-style` | load / write a YAML/JSON style file |
+| `--analytics` | also write per-family statistics as CSV/JSON |
+| `--no-titles` | omit titles from the exported figure and analytics-chart images |
+| `-cen` | draw centromeres |
+
+### Input formats
+
+* **Table** — columns `gene_id, gene_family, chromosome, start, end, strand`
+  (1-based, inclusive; header synonyms accepted). A `centromere` value in
+  `gene_family` (strand `0`) marks a centromere.
+* **BED** — 0-based half-open, converted automatically. One file → column 4 is
+  the family; several files → each file's base name is the family; one file plus
+  a mapping file → family from the map.
+* **GFF3 / GTF** — 1-based; gene-like feature types kept; family taken from
+  `--family-attr` (default search: `gene_family`, `Family`, `gene_biotype`,
+  `Name`, …).
+
+### Analytics
+
+`--analytics` writes `analytics_*.csv` / `.bed`, `analytics_summary.json` and
+four figures (`analytics_genes_per_family`, `analytics_positional_profile`,
+`analytics_ripley`, `analytics_family_proximity` — one per requested figure
+format). It computes:
+
+* per-family counts split into genes on chromosomes vs. unplaced/stray contigs,
+  linear density, gene length, strand fraction;
+* permutation tests for **telomere-** and (with a centromere track)
+  **centromere-proximal** bias, plus **p-arm / q-arm** occupancy;
+* **tandem-array** detection and a **tandem / proximal / dispersed** duplication
+  mode per family;
+* **multi-scale clustering** — edge-corrected 1-D **Ripley's K/L** with a
+  permutation envelope (`--ripley-scales`);
+* **chromosome-enrichment** (binomial, per family × chromosome), **strand bias**,
+  and per-chromosome **family diversity** (Shannon / evenness);
+* a binned **positional density profile** ("metachromosome" plot);
+* a **family × family proximity matrix** with average-linkage clustering;
+* **multigene-family hotspots** — a Poisson window scan, merged and written as a
+  table and a **BED** file (`--hotspot-window`);
+* optional pairwise **co-localization** (`--colocalization`).
+
+Every per-family / per-pair / per-window test carries a Benjamini–Hochberg
+`q_value`. See `templates/help.html` (the *Downloadable outputs* section) for the
+column-by-column layout of each file.
+
+## Web portal
+
+```bash
+# development
+python flaskapp.py                       # http://localhost:5001
+
+# production
+gunicorn -w 1 --threads 4 -b 0.0.0.0:5001 "gfviewer_web:create_app()"
+```
+
+Uploads are rendered on a background thread pool behind an async job API
+(`POST /api/jobs` → `GET /api/jobs/<id>/status` → results page). The results page
+embeds the SVG with an editor for choosing which families and chromosomes to
+draw, recolouring, moving the legend and labels, changing fonts and mark style,
+toggling whether titles are baked into the image files, then re-rendering and
+exporting. Analytics figures are shown inline, and two buttons download
+**everything as a ZIP** — either as produced, or re-rendered in every figure
+format. `GET /api/health` is a readiness probe.
+
+**Usage monitor.** A privacy-respecting counter (`/stats`, or JSON at
+`/api/stats`) tracks page views, unique visitors per day (a salted daily hash —
+no IPs, cookies or other personal data are stored), jobs submitted / completed /
+failed, example-dataset runs and downloads, with a rolling ~120-day daily
+series. Counters persist to `instance/usage.json`.
+
+Configuration (environment variables): `GFVIEWER_DATA_DIR`,
+`GFVIEWER_MAX_UPLOAD_MB` (25), `GFVIEWER_WORKERS` (2), `GFVIEWER_JOB_TTL_HOURS`
+(24), `GFVIEWER_USAGE_FILE`, `GFVIEWER_STATS_TOKEN` (require `?token=` on
+`/stats`), `SECRET_KEY`, `PORT`.
+
+## Example datasets
+
+`python tests/make_fixtures.py` builds every bundled dataset into
+`static/tests/`: the three *Babesia* sets, the 6-family set re-expressed in
+every input format (`formats/` — BED, per-family BED, BED + mapping, GFF3, GTF),
+and two synthetic sets — 10 random gene families on the *Arabidopsis* (TAIR10)
+chromosomes and 20 on *C. elegans* (WBcel235). The web home page lists them all
+with **Run** (submits the job) and **Download** buttons, plus *Download every
+dataset (ZIP)*.
+
+## Tests
+
+```bash
+python tests/make_fixtures.py            # once, to build the example datasets
+pytest -q
+```
+
+## Citation
+
+Chakravarty S. & Lonardi S. *Visualizing the localization of multigene families
+with GFViewer.* Development supported by NIH grant 1-R01-AI169543-01.

gfviewer-2.0.0/docs/BIOCONDA.md

@@ -0,0 +1,197 @@
+# Releasing GFViewer on Bioconda
+
+GFViewer is packaged on **Bioconda** (channel `bioconda`), recipe at
+`bioconda/bioconda-recipes` → `recipes/gfviewer/meta.yaml`. Recipe maintainer:
+`sakshar`. The package is `noarch: python` and ships the **CLI only**
+(`gfviewer` command); the Flask web portal (`pip install "gfviewer[web]"`) is
+not part of the conda package.
+
+Install (Bioconda requires conda-forge in the channel list):
+
+```bash
+conda install -c conda-forge -c bioconda gfviewer
+# or
+mamba install -c conda-forge -c bioconda gfviewer
+```
+
+---
+
+## How a release reaches Bioconda
+
+1. You push a new tag `vX.Y.Z` to `github.com/sakshar/GFViewer` and cut a GitHub
+   Release.
+2. **BiocondaBot** notices the new tag within a few hours and opens an
+   auto-bump PR against `bioconda-recipes` titled *"Update gfviewer to X.Y.Z"*.
+   It changes only `version`, `source.url`, `source.sha256` and resets
+   `build.number` to `0`.
+3. Bioconda CI builds the recipe on Linux / OSX / ARM. When green **and a
+   maintainer approves**, it is merged and the build bot uploads the package to
+   `anaconda.org/bioconda/gfviewer` (usually 30–60 min after merge).
+
+The auto-bump PR does **not** update dependencies or metadata — do that in a
+separate follow-up PR (see below) whenever `pyproject.toml` deps change.
+
+---
+
+## Step 1 — Merge the auto-bump PR
+
+On the BiocondaBot PR page (e.g. `bioconda/bioconda-recipes#68787` for 2.0.0):
+
+1. Check that all CI checks are green (Linux Tests, OSX-64 Tests,
+   build and test (ARM), Lint).
+2. Verify the `sha256` matches the tag tarball:
+
+   ```bash
+   curl -sL https://github.com/sakshar/GFViewer/archive/refs/tags/vX.Y.Z.tar.gz | shasum -a 256
+   ```
+
+   > GitHub's auto-generated tag tarballs are **not guaranteed byte-stable**,
+   > and force-moving a tag changes the hash. If the hashes differ, comment
+   > `@BiocondaBot please update` on the PR (or fix `sha256` by hand). Long
+   > term, once GFViewer is on PyPI, switch `source.url` to the immutable PyPI
+   > sdist: `https://pypi.io/packages/source/g/gfviewer/gfviewer-{{ version }}.tar.gz`.
+
+3. As the recipe maintainer, comment to merge:
+
+   ```
+   @BiocondaBot please merge
+   ```
+
+---
+
+## Step 2 — Follow-up PR to update `meta.yaml` (deps / metadata)
+
+Do this **after** the auto-bump PR is merged, so you branch off an up-to-date
+`master`. `bioconda-recipes` is huge — edit the single file in the browser
+rather than cloning.
+
+### Web UI (recommended)
+
+1. Open
+   `https://github.com/bioconda/bioconda-recipes/blob/master/recipes/gfviewer/meta.yaml`
+   and confirm `version:` is the new one.
+2. Click the **pencil** ("Edit this file"). GitHub prompts to **fork the
+   repository** (one-time) — accept.
+3. Apply your changes (see the reference `meta.yaml` below).
+4. **Bump `build.number`** by 1 (a recipe change without a version change needs
+   a new build number; the auto-bump already set it to `0` for the version
+   change, so a same-version follow-up becomes `1`).
+5. Commit message e.g. `gfviewer: add numpy, pillow, pyyaml to run deps (build 1)`
+   → **"Create a new branch and start a pull request"** → branch
+   `gfviewer-deps` → **Propose changes**.
+6. Base must be `bioconda:master`. Complete the PR template checklist
+   (one recipe changed; build number bumped).
+7. When CI is green and approved: `@BiocondaBot please merge`.
+
+### Local git (alternative)
+
+```bash
+# Fork bioconda/bioconda-recipes on GitHub first, then:
+git clone --depth 1 https://github.com/<your-username>/bioconda-recipes.git
+cd bioconda-recipes
+git remote add upstream https://github.com/bioconda/bioconda-recipes.git
+git checkout -b gfviewer-deps
+
+$EDITOR recipes/gfviewer/meta.yaml        # apply the changes
+
+git add recipes/gfviewer/meta.yaml
+git commit -m "gfviewer: add numpy, pillow, pyyaml to run deps (build 1)"
+git push -u origin gfviewer-deps
+# open the PR: <you>:gfviewer-deps  ->  bioconda:master
+```
+
+No local build needed — Bioconda CI builds it. (A local `conda build` of a
+Bioconda recipe needs `bioconda-utils` and is heavy.)
+
+---
+
+## Reference `meta.yaml` for GFViewer v2.x
+
+Keep `requirements.run` in sync with `[project.dependencies]` in
+`pyproject.toml`. As of v2.0.0 that is: biopython, matplotlib, pandas, numpy,
+openpyxl, Pillow, reportlab, PyPDF2, PyYAML. On conda: `matplotlib` →
+`matplotlib-base` (headless), `PyPDF2` → `pypdf2`, `Pillow` → `pillow`,
+`PyYAML` → `pyyaml`.
+
+```yaml
+package:
+  name: gfviewer
+  version: "2.0.0"
+
+source:
+  url: https://github.com/sakshar/GFViewer/archive/refs/tags/v2.0.0.tar.gz
+  sha256: 30aec61635d669ac86f9596b254646bf1cff3544bc033fe87d0d376510e94c5f
+
+build:
+  noarch: python
+  number: 1                     # bump on any recipe change without a version change
+  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv"
+  run_exports:
+    - {{ pin_subpackage("gfviewer", max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.8,<3.13
+    - pip
+    - setuptools >=64
+    - wheel
+  run:
+    - python >=3.8,<3.13
+    - biopython
+    - pandas
+    - numpy                     # imported directly by gfviewer.analytics
+    - matplotlib-base
+    - pillow                    # matplotlib-base excludes it; needed for -f jpg / tiff
+    - reportlab
+    - pypdf2
+    - openpyxl
+    - pyyaml                    # --style / --save-style *.yaml
+
+test:
+  imports:
+    - gfviewer                  # do NOT test `import gfviewer_web` (needs Flask, not a dep)
+  commands:
+    - gfviewer --help
+    - gfviewer --version
+
+about:
+  home: https://github.com/sakshar/GFViewer
+  license: MIT
+  license_file: LICENSE
+  summary: "Visualize and quantify the localization of multigene families across chromosomes."
+  description: |
+    GFViewer draws round-capped chromosome ideograms with each gene family in
+    its own colour and computes localization statistics (sub-telomeric bias,
+    tandem arrays, 1-D Ripley's K/L, chromosome enrichment, multigene-family
+    hotspots, family-proximity clustering, ...). Reads annotation tables, BED,
+    GFF3 and GTF. Provides the `gfviewer` command-line tool.
+  dev_url: https://github.com/sakshar/GFViewer
+
+extra:
+  recipe-maintainers:
+    - sakshar
+```
+
+---
+
+## Checklist for the next version bump (vX.Y.Z)
+
+- [ ] `gfviewer/__init__.py::__version__` and `pyproject.toml::version` bumped
+      together (`tests/test_packaging.py` fails if they drift).
+- [ ] Tag `vX.Y.Z` pushed; GitHub Release published.
+- [ ] Wait for the BiocondaBot *"Update gfviewer to X.Y.Z"* PR.
+- [ ] Confirm `sha256` matches `curl -sL <tag tarball> | shasum -a 256`.
+- [ ] If `pyproject.toml` deps changed, prepare the `meta.yaml` `run:` update.
+- [ ] `@BiocondaBot please merge` once green + approved.
+- [ ] Follow-up PR for deps/metadata if needed (`build.number` +1).
+- [ ] After the channel updates: `conda install -c conda-forge -c bioconda gfviewer`
+      and check `gfviewer --version`.
+
+## Useful BiocondaBot / PR commands
+
+| Comment | Effect |
+|---|---|
+| `@BiocondaBot please merge` | maintainer merges a green, approved PR |
+| `@BiocondaBot please update` | regenerate the bump PR (re-fetch source, recompute hash) |
+| `@BiocondaBot please add label` | add the `please review & merge` label |
+| `@bioconda-bot please fetch artifacts` | link to the built packages from CI for local testing |