allelix 1.8.1__tar.gz → 1.8.3__tar.gz

{allelix-1.8.1 → allelix-1.8.3}/PKG-INFO

@@ -1,11 +1,13 @@
 Metadata-Version: 2.4
 Name: allelix
-Version: 1.8.1
+Version: 1.8.3
 Summary: Open-source genotype analysis toolkit. Format-agnostic ingestion, database-agnostic annotation, offline-first.
 Author-email: dial481 <dial481@users.noreply.github.com>
 License-Expression: AGPL-3.0-or-later
-Project-URL: Homepage, https://github.com/dial481/allelix
+Project-URL: Homepage, https://allelix.io
+Project-URL: Source, https://github.com/dial481/allelix
 Project-URL: Issues, https://github.com/dial481/allelix/issues
+Project-URL: Changelog, https://github.com/dial481/allelix/blob/main/CHANGELOG.md
 Keywords: genomics,genotype,snp,bioinformatics,dna
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
@@ -42,54 +44,27 @@ Open-source command-line toolkit for analyzing raw genotype files from consumer
 > HTML/JSON/terminal reports, methylation + pharmacogenomics focused
 > commands, report diffing, persistent config with commercial-mode
 > safety switch. Build auto-detection from position data (ADR-0021).
-> No regex on prose anywhere in production. **Latest: v1.7.0** — PLINK
-> export, magnitude scoring formalization (ADR-0034). Release notes:
-> [`CHANGELOG.md`](CHANGELOG.md).
+> No regex on prose anywhere in production. **Latest: v1.8.3** —
+> pip install quickstart, workflow hardening, PyPI link fix.
+> Release notes:
+> [`CHANGELOG.md`](https://github.com/dial481/allelix/blob/main/CHANGELOG.md).
 
 ## Quickstart
 
-Requires Python 3.11+.
-
 ```bash
-git clone https://github.com/dial481/allelix
-cd allelix
-python -m venv .venv
-source .venv/bin/activate
-pip install -e ".[dev]"
-
-# Generate a synthetic test fixture
-python tests/generate_mock_data.py
-
-# Show summary statistics for a genotype file
-allelix stats tests/fixtures/mock_myhappygenes.txt
+pip install allelix
 
-# Download reference databases. First run downloads all sources (~15GB
-# on disk with gnomAD + AlphaMissense). Use --no-gnomad / --no-alphamissense
-# to skip the large enrichment databases. Re-runs skip unchanged sources.
+# Download reference databases (~15GB with all sources).
+# Use --no-gnomad / --no-alphamissense to skip the large ones.
 # CADD is opt-in: allelix db update --cadd
 allelix db update
-allelix db status   # see what's cached
 
-# Analyze a genotype file against all ready databases
-allelix analyze tests/fixtures/mock_myhappygenes.txt --min-magnitude 5
-
-# Same data, focused subsets
-allelix methylation tests/fixtures/mock_myhappygenes.txt
-allelix pharmacogenomics tests/fixtures/mock_myhappygenes.txt
-
-# Compare two genotype files (coverage, concordance, strand-flip detection)
-allelix compare file1.txt file2.txt
-
-# Export to PLINK1 binary format (.bed/.bim/.fam) for plink2, ADMIXTURE, PRSice
-# Expect ~60% monomorphic markers (A2=0) — genotyping chips probe many
-# intronic/intergenic sites outside gnomAD's exome coverage.
-allelix export plink genotype_file.txt -o output_prefix --build grch37
-
-# Output to a self-contained HTML or JSON report
-allelix analyze tests/fixtures/mock_myhappygenes.txt --output report.html
-allelix analyze tests/fixtures/mock_myhappygenes.txt --output report.json
+# Analyze a genotype file
+allelix analyze your_genotype_file.txt --output report.html
 ```
 
+Requires Python 3.11+. See [Development](#development) for source installs and running tests.
+
 ## Supported Formats
 
 | Format | Status | Notes |
@@ -243,7 +218,7 @@ None of these are scraping errors. They are editorial inconsistencies on the sou
 
 ## Architecture & Design Decisions
 
-The "why" behind major design choices lives in [`docs/adr/`](docs/adr/README.md) as Architecture Decision Records. Read these before proposing changes that touch the parser/annotator interfaces, the regulatory posture, or the data-handling model.
+The "why" behind major design choices lives in [`docs/adr/`](https://github.com/dial481/allelix/blob/main/docs/adr/README.md) as Architecture Decision Records. Read these before proposing changes that touch the parser/annotator interfaces, the regulatory posture, or the data-handling model.
 
 Notable load-bearing ADRs:
 
@@ -253,7 +228,7 @@ Notable load-bearing ADRs:
 - **ADR-0009 — PharmGKB matches the user's exact normalized diploid call.**
 - **ADR-0015 — Mock data generators are the contract.** Fixture shape must mirror real data shape; invariants tested.
 
-Release history: see [`CHANGELOG.md`](CHANGELOG.md).
+Release history: see [`CHANGELOG.md`](https://github.com/dial481/allelix/blob/main/CHANGELOG.md).
 
 ## Development
 

{allelix-1.8.1 → allelix-1.8.3}/README.md

@@ -10,54 +10,27 @@ Open-source command-line toolkit for analyzing raw genotype files from consumer
 > HTML/JSON/terminal reports, methylation + pharmacogenomics focused
 > commands, report diffing, persistent config with commercial-mode
 > safety switch. Build auto-detection from position data (ADR-0021).
-> No regex on prose anywhere in production. **Latest: v1.7.0** — PLINK
-> export, magnitude scoring formalization (ADR-0034). Release notes:
-> [`CHANGELOG.md`](CHANGELOG.md).
+> No regex on prose anywhere in production. **Latest: v1.8.3** —
+> pip install quickstart, workflow hardening, PyPI link fix.
+> Release notes:
+> [`CHANGELOG.md`](https://github.com/dial481/allelix/blob/main/CHANGELOG.md).
 
 ## Quickstart
 
-Requires Python 3.11+.
-
 ```bash
-git clone https://github.com/dial481/allelix
-cd allelix
-python -m venv .venv
-source .venv/bin/activate
-pip install -e ".[dev]"
-
-# Generate a synthetic test fixture
-python tests/generate_mock_data.py
-
-# Show summary statistics for a genotype file
-allelix stats tests/fixtures/mock_myhappygenes.txt
+pip install allelix
 
-# Download reference databases. First run downloads all sources (~15GB
-# on disk with gnomAD + AlphaMissense). Use --no-gnomad / --no-alphamissense
-# to skip the large enrichment databases. Re-runs skip unchanged sources.
+# Download reference databases (~15GB with all sources).
+# Use --no-gnomad / --no-alphamissense to skip the large ones.
 # CADD is opt-in: allelix db update --cadd
 allelix db update
-allelix db status   # see what's cached
 
-# Analyze a genotype file against all ready databases
-allelix analyze tests/fixtures/mock_myhappygenes.txt --min-magnitude 5
-
-# Same data, focused subsets
-allelix methylation tests/fixtures/mock_myhappygenes.txt
-allelix pharmacogenomics tests/fixtures/mock_myhappygenes.txt
-
-# Compare two genotype files (coverage, concordance, strand-flip detection)
-allelix compare file1.txt file2.txt
-
-# Export to PLINK1 binary format (.bed/.bim/.fam) for plink2, ADMIXTURE, PRSice
-# Expect ~60% monomorphic markers (A2=0) — genotyping chips probe many
-# intronic/intergenic sites outside gnomAD's exome coverage.
-allelix export plink genotype_file.txt -o output_prefix --build grch37
-
-# Output to a self-contained HTML or JSON report
-allelix analyze tests/fixtures/mock_myhappygenes.txt --output report.html
-allelix analyze tests/fixtures/mock_myhappygenes.txt --output report.json
+# Analyze a genotype file
+allelix analyze your_genotype_file.txt --output report.html
 ```
 
+Requires Python 3.11+. See [Development](#development) for source installs and running tests.
+
 ## Supported Formats
 
 | Format | Status | Notes |
@@ -211,7 +184,7 @@ None of these are scraping errors. They are editorial inconsistencies on the sou
 
 ## Architecture & Design Decisions
 
-The "why" behind major design choices lives in [`docs/adr/`](docs/adr/README.md) as Architecture Decision Records. Read these before proposing changes that touch the parser/annotator interfaces, the regulatory posture, or the data-handling model.
+The "why" behind major design choices lives in [`docs/adr/`](https://github.com/dial481/allelix/blob/main/docs/adr/README.md) as Architecture Decision Records. Read these before proposing changes that touch the parser/annotator interfaces, the regulatory posture, or the data-handling model.
 
 Notable load-bearing ADRs:
 
@@ -221,7 +194,7 @@ Notable load-bearing ADRs:
 - **ADR-0009 — PharmGKB matches the user's exact normalized diploid call.**
 - **ADR-0015 — Mock data generators are the contract.** Fixture shape must mirror real data shape; invariants tested.
 
-Release history: see [`CHANGELOG.md`](CHANGELOG.md).
+Release history: see [`CHANGELOG.md`](https://github.com/dial481/allelix/blob/main/CHANGELOG.md).
 
 ## Development
 

{allelix-1.8.1 → allelix-1.8.3}/allelix/models.py

@@ -79,7 +79,9 @@ class Annotation:
         magnitude: 0-10 importance score (SNPedia-style).
         description: Human-readable explanation.
         attribution: Display name of the source ("ClinVar", "PharmGKB", ...).
-        genotype_match: Which genotype triggers this annotation (e.g., "T/T").
+        genotype_match: Which genotype triggers this annotation. For SNVs this
+            is a concatenated, sorted allele pair (e.g., "AG", "TT"); the slash
+            form (e.g., "AT/A") appears only for indels.
         references: PubMed IDs or URLs supporting the claim.
         condition: Disease or condition name, if applicable.
         gene: Gene symbol, if known.

{allelix-1.8.1 → allelix-1.8.3}/allelix/reports/html.py

@@ -101,6 +101,7 @@ _CSS = """\
   --notice-border: #f9a825;
   --notice-warn-bg: #fff3e0;
   --notice-warn-border: #e65100;
+  --link: #1976d2;
 }
 @media (prefers-color-scheme: dark) {
   :root:not([data-theme="light"]) {
@@ -119,6 +120,7 @@ _CSS = """\
     --notice-border: #f9a825;
     --notice-warn-bg: #331a00;
     --notice-warn-border: #e65100;
+    --link: #93c5fd;
   }
 }
 [data-theme="dark"] {
@@ -137,6 +139,7 @@ _CSS = """\
   --notice-border: #f9a825;
   --notice-warn-bg: #331a00;
   --notice-warn-border: #e65100;
+  --link: #93c5fd;
 }
 
 *, *::before, *::after { box-sizing: border-box; }
@@ -152,6 +155,7 @@ body {
 }
 h1 { margin-bottom: .25rem; }
 .subtitle { color: var(--text-muted); margin-top: 0; }
+a { color: var(--link); }
 
 .notice {
   background: var(--notice-bg, #fff8e1); border-left: 4px solid var(--notice-border, #f9a825);
@@ -1024,7 +1028,7 @@ def render_html(
             '<th data-sort="gene" class="sortable">'
             'Gene<span class="sort-arrow"></span></th>'
             '<th data-sort="genotype" class="sortable">'
-            'Genotype<span class="sort-arrow"></span></th>'
+            'GT<span class="sort-arrow"></span></th>'
             '<th data-sort="repute" class="sortable">'
             'Repute<span class="sort-arrow"></span></th>'
             "<th>Summary</th>"
@@ -1090,16 +1094,25 @@ def render_html(
         "<html lang='en'><head><meta charset='utf-8'>"
         '<meta name="viewport" content="width=device-width, initial-scale=1">'
         '<link rel="icon" type="image/svg+xml" href="data:image/svg+xml,'
-        "<svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 32 32'>"
-        "<defs><linearGradient id='g' x1='0' y1='0' x2='1' y2='1'>"
-        "<stop offset='0%25' stop-color='%234f46e5'/>"
-        "<stop offset='100%25' stop-color='%2306b6d4'/>"
-        "</linearGradient></defs>"
-        "<path d='M16 2C9 2 8 8 8 8s2-3 8-3 8 3 8 3-1-6-8-6z"
-        "m0 6c-7 0-8 6-8 6s2-3 8-3 8 3 8 3-1-6-8-6z"
-        "m0 6c-7 0-8 6-8 6s2-3 8-3 8 3 8 3-1-6-8-6z"
-        "m0 6c-7 0-8 6-8 6s2-3 8-3 8 3 8 3-1-6-8-6z'"
-        " fill='url(%23g)' opacity='0.9'/></svg>\">"
+        "%3Csvg viewBox='0 0 32 32' fill='none'"
+        " xmlns='http://www.w3.org/2000/svg'%3E"
+        "%3Ccircle cx='16' cy='16' r='14' stroke='%236366f1'"
+        " stroke-width='1.5' opacity='0.3'/%3E"
+        "%3Cpath d='M10 6C10 6 22 12 22 16C22 20 10 26 10 26'"
+        " stroke='%236366f1' stroke-width='2'"
+        " stroke-linecap='round' fill='none'/%3E"
+        "%3Cpath d='M22 6C22 6 10 12 10 16C10 20 22 26 22 26'"
+        " stroke='%236366f1' stroke-width='2'"
+        " stroke-linecap='round' fill='none' opacity='0.4'/%3E"
+        "%3Ccircle cx='10' cy='10' r='2' fill='%236366f1'/%3E"
+        "%3Ccircle cx='22' cy='10' r='2' fill='%236366f1'"
+        " opacity='0.4'/%3E"
+        "%3Ccircle cx='16' cy='16' r='2' fill='%236366f1'"
+        " opacity='0.7'/%3E"
+        "%3Ccircle cx='22' cy='22' r='2' fill='%236366f1'/%3E"
+        "%3Ccircle cx='10' cy='22' r='2' fill='%236366f1'"
+        " opacity='0.4'/%3E"
+        '%3C/svg%3E">'
         f"<title>{_escape(title)}</title>"
         f"<style>{_CSS}</style>"
         "</head><body>"

{allelix-1.8.1 → allelix-1.8.3}/allelix.egg-info/PKG-INFO

@@ -1,11 +1,13 @@
 Metadata-Version: 2.4
 Name: allelix
-Version: 1.8.1
+Version: 1.8.3
 Summary: Open-source genotype analysis toolkit. Format-agnostic ingestion, database-agnostic annotation, offline-first.
 Author-email: dial481 <dial481@users.noreply.github.com>
 License-Expression: AGPL-3.0-or-later
-Project-URL: Homepage, https://github.com/dial481/allelix
+Project-URL: Homepage, https://allelix.io
+Project-URL: Source, https://github.com/dial481/allelix
 Project-URL: Issues, https://github.com/dial481/allelix/issues
+Project-URL: Changelog, https://github.com/dial481/allelix/blob/main/CHANGELOG.md
 Keywords: genomics,genotype,snp,bioinformatics,dna
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
@@ -42,54 +44,27 @@ Open-source command-line toolkit for analyzing raw genotype files from consumer
 > HTML/JSON/terminal reports, methylation + pharmacogenomics focused
 > commands, report diffing, persistent config with commercial-mode
 > safety switch. Build auto-detection from position data (ADR-0021).
-> No regex on prose anywhere in production. **Latest: v1.7.0** — PLINK
-> export, magnitude scoring formalization (ADR-0034). Release notes:
-> [`CHANGELOG.md`](CHANGELOG.md).
+> No regex on prose anywhere in production. **Latest: v1.8.3** —
+> pip install quickstart, workflow hardening, PyPI link fix.
+> Release notes:
+> [`CHANGELOG.md`](https://github.com/dial481/allelix/blob/main/CHANGELOG.md).
 
 ## Quickstart
 
-Requires Python 3.11+.
-
 ```bash
-git clone https://github.com/dial481/allelix
-cd allelix
-python -m venv .venv
-source .venv/bin/activate
-pip install -e ".[dev]"
-
-# Generate a synthetic test fixture
-python tests/generate_mock_data.py
-
-# Show summary statistics for a genotype file
-allelix stats tests/fixtures/mock_myhappygenes.txt
+pip install allelix
 
-# Download reference databases. First run downloads all sources (~15GB
-# on disk with gnomAD + AlphaMissense). Use --no-gnomad / --no-alphamissense
-# to skip the large enrichment databases. Re-runs skip unchanged sources.
+# Download reference databases (~15GB with all sources).
+# Use --no-gnomad / --no-alphamissense to skip the large ones.
 # CADD is opt-in: allelix db update --cadd
 allelix db update
-allelix db status   # see what's cached
 
-# Analyze a genotype file against all ready databases
-allelix analyze tests/fixtures/mock_myhappygenes.txt --min-magnitude 5
-
-# Same data, focused subsets
-allelix methylation tests/fixtures/mock_myhappygenes.txt
-allelix pharmacogenomics tests/fixtures/mock_myhappygenes.txt
-
-# Compare two genotype files (coverage, concordance, strand-flip detection)
-allelix compare file1.txt file2.txt
-
-# Export to PLINK1 binary format (.bed/.bim/.fam) for plink2, ADMIXTURE, PRSice
-# Expect ~60% monomorphic markers (A2=0) — genotyping chips probe many
-# intronic/intergenic sites outside gnomAD's exome coverage.
-allelix export plink genotype_file.txt -o output_prefix --build grch37
-
-# Output to a self-contained HTML or JSON report
-allelix analyze tests/fixtures/mock_myhappygenes.txt --output report.html
-allelix analyze tests/fixtures/mock_myhappygenes.txt --output report.json
+# Analyze a genotype file
+allelix analyze your_genotype_file.txt --output report.html
 ```
 
+Requires Python 3.11+. See [Development](#development) for source installs and running tests.
+
 ## Supported Formats
 
 | Format | Status | Notes |
@@ -243,7 +218,7 @@ None of these are scraping errors. They are editorial inconsistencies on the sou
 
 ## Architecture & Design Decisions
 
-The "why" behind major design choices lives in [`docs/adr/`](docs/adr/README.md) as Architecture Decision Records. Read these before proposing changes that touch the parser/annotator interfaces, the regulatory posture, or the data-handling model.
+The "why" behind major design choices lives in [`docs/adr/`](https://github.com/dial481/allelix/blob/main/docs/adr/README.md) as Architecture Decision Records. Read these before proposing changes that touch the parser/annotator interfaces, the regulatory posture, or the data-handling model.
 
 Notable load-bearing ADRs:
 
@@ -253,7 +228,7 @@ Notable load-bearing ADRs:
 - **ADR-0009 — PharmGKB matches the user's exact normalized diploid call.**
 - **ADR-0015 — Mock data generators are the contract.** Fixture shape must mirror real data shape; invariants tested.
 
-Release history: see [`CHANGELOG.md`](CHANGELOG.md).
+Release history: see [`CHANGELOG.md`](https://github.com/dial481/allelix/blob/main/CHANGELOG.md).
 
 ## Development
 

{allelix-1.8.1 → allelix-1.8.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "allelix"
-version = "1.8.1"
+version = "1.8.3"
 description = "Open-source genotype analysis toolkit. Format-agnostic ingestion, database-agnostic annotation, offline-first."
 readme = "README.md"
 requires-python = ">=3.11"
@@ -42,8 +42,10 @@ dev = [
 allelix = "allelix.cli:main"
 
 [project.urls]
-Homepage = "https://github.com/dial481/allelix"
+Homepage = "https://allelix.io"
+Source = "https://github.com/dial481/allelix"
 Issues = "https://github.com/dial481/allelix/issues"
+Changelog = "https://github.com/dial481/allelix/blob/main/CHANGELOG.md"
 
 [tool.setuptools.packages.find]
 include = ["allelix*"]