Merge pull request #5 from cfe-lab/FoldClinicalIn

Continuing to consolidate the HLA algorithm again

Author: rhliang

.devcontainer/devcontainer.json

@@ -19,35 +19,29 @@
 	"updateRemoteUserUID": true,
 	"containerEnv": {
 		"WORKON_HOME": "${containerWorkspaceFolder}/.venv",
-		"PYTHONPATH": "${containerWorkspaceFolder}",
-		"ORACLE_HOME": "/opt/oracle/instantclient",
-		"LD_LIBRARY_PATH": "/opt/oracle/instantclient"
+		"PYTHONPATH": "${containerWorkspaceFolder}"
 	},
 	"onCreateCommand": {
 		"update apt": [
 			"/usr/bin/apt",
 			"update"
-		],
-		"sync venv/install if missing": [
-			"/usr/local/bin/uv",
-			"sync",
-			"--frozen"
 		]
+		// "sync venv/install if missing": [
+		// 	"/usr/local/bin/uv",
+		// 	"sync",
+		// 	"--frozen"
+		// ]
 	},
 	"postCreateCommand": {
-		"install ssh client": [
+		"install apt packages": [
 			"/usr/bin/apt",
 			"install",
 			"--no-install-recommends",
 			"-y",
 			"openssh-client",
 			"libaio-dev",
-			"unzip"
-		],
-		"install Instant Client": [
-			"/usr/bin/env",
-			"bash",
-			"${containerWorkspaceFolder}/.devcontainer/install_instant_client.bash"
+			"unzip",
+			"yamllint"
 		],
 		"install Ruby": [
 			"/usr/bin/apt",

.devcontainer/install_instant_client.bash

@@ -47,15 +47,19 @@ jobs:
       - name: Run tests
         run: uv run pytest --junitxml=pytest.xml
 
-# TODO: Look into github actions, these are out of date
-# - name: Upload coverage data
-#   uses: actions/upload-artifact@v3
-#   with:
-#     name: coverage-data
-#     path: coverage.xml
-
-# - name: Publish Test Report
-#   uses: mikepenz/action-junit-report@v3
-#   if: success() || failure()
-#   with:
-#     report_paths: unit_test.xml
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      # - name: Publish Test Report
+      #   uses: mikepenz/action-junit-report@v5
+      #   if: success() || failure()
+      #   with:
+      #     report_paths: pytest.xml
+
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test.yml

@@ -1,7 +1,7 @@
 ignore:
   - .git/*
   - .venv/*
-  - src/easyhla/default_data/hla_standards.yaml
+  - src/hla_algorithm/default_data/hla_standards.yaml
 
 extends: default
 

.yamllint.yml

@@ -1,17 +1,19 @@
-# pyEasyHLA
+# BC-CfE HLA algorithm
 
-[![pipeline status](https://git-int.cfenet.ubc.ca/drickett/pyeasyhla/badges/main/pipeline.svg)](https://git-int.cfenet.ubc.ca/drickett/pyeasyhla/-/commits/main)
-[![coverage report](https://git-int.cfenet.ubc.ca/drickett/pyeasyhla/badges/main/coverage.svg)](https://git-int.cfenet.ubc.ca/drickett/pyeasyhla/-/commits/main)
-[![Latest Release](https://git-int.cfenet.ubc.ca/drickett/pyeasyhla/-/badges/release.svg)](https://git-int.cfenet.ubc.ca/drickett/pyeasyhla/-/releases)
-
-[[_TOC_]]
+[![test](https://github.com/cfe-lab/hla_algorithm/actions/workflows/test.yml/badge.svg)](https://github.com/cfe-lab/hla_algorithm/actions/workflows/test.yml)
+[![codecov](https://codecov.io/gh/cfe-lab/hla_algorithm/graph/badge.svg?token=ZJQKPBRTQB)](https://codecov.io/gh/cfe-lab/hla_algorithm)
+![GitHub Release](https://img.shields.io/github/v/release/cfe-lab/hla_algorithm?sort=semver)
 
 ## Objective
 
-This is a python implementation of [BBLab's hla-easy.rb](https://github.com/cfe-lab/bblab-server/blob/main/alldata/hla_class/hla-easy.rb) file. The goal is to remove the ruby dependency from BBLab.
+This is a Python implementation of the BC-CfE HLA algorithm.  This algorithm has
+several interpretations, including [BBLab's hla-easy.rb](https://github.com/cfe-lab/bblab-server/blob/main/alldata/hla_class/hla-easy.rb) file.  This project aims
+to consolidate all of our HLA algorithm versions into a single version.
 
 ## Testing
 
+FIXME
+
 The current validation method is to go to the [BBLab HLA Class tool page](https://hivresearchtools.bccfe.ca/django/tools/hla_class/), upload [test.fasta](https://github.com/cfe-lab/bblab-server/blob/main/tests/test.fasta) in `HLA Type C`, and assert that its output matches [the output kept in version control](https://github.com/cfe-lab/bblab-server/blob/main/tests/hla_class/HLA-C%20batch%20mode%20test%20data%20OUTPUT.csv).
 
 ## TODO

README.md

@@ -3,7 +3,7 @@ requires = ["hatchling", "uv-dynamic-versioning"]
 build-backend = "hatchling.build"
 
 [project]
-name = "easyhla"
+name = "hla_algorithm"
 description = ''
 readme = "README.md"
 requires-python = ">=3.10"
@@ -29,20 +29,17 @@ dependencies = [
   "numpy>=2.2.3",
   "pydantic>=2.10.6",
   "pydantic-numpy>=8.0.1",
-  "pytz>=2025.1",
   "pyyaml>=6.0.2",
   "requests>=2.32.3",
   "typer>=0.15.2",
   "types-pyyaml>=6.0.12.20250516",
   "types-requests>=2.32.4.20250611",
-  "uv-dynamic-versioning>=0.8.2",
 ]
 
 [dependency-groups]
 dev = [
   "mypy>=1.15.0",
   "mypy-extensions>=1.0.0",
-  "oracledb>=3.1.0",
   "pandas>=2.2.3",
   "pandas-stubs>=2.2.3.241126",
   "pre-commit>=4.1.0",
@@ -52,47 +49,38 @@ dev = [
   "pytest-mock>=3.14.0",
   "pytest-xdist>=3.6.1",
   "ruff>=0.9.9",
-  "sqlalchemy>=2.0.40",
-  "types-pytz>=2025.1.0.20250204",
+  "uv-dynamic-versioning>=0.8.2",
 ]
 
 [project.urls]
-Documentation = "https://github.com/cfe-lab/pyeasyhla/blob/main/README.md"
-Issues = "https://github.com/cfe-lab/pyeasyhla/issues"
-Source = "https://github.com/cfe-lab/pyeasyhla"
+Documentation = "https://github.com/cfe-lab/hla_algorithm/blob/main/README.md"
+Issues = "https://github.com/cfe-lab/hla_algorithm/issues"
+Source = "https://github.com/cfe-lab/hla_algorithm"
 
 [project.scripts]
-clinical_hla = "easyhla.clinical_hla:main"
-interpret_from_json = "easyhla.interpret_from_json:main"
-bblab = "easyhla.bblab:main"
-update_alleles = "easyhla.update_alleles:main"
-update_frequency_file = "easyhla.update_frequency_file:main"
-
-[project.optional-dependencies]
-database = [
-    "oracledb>=3.1.0",
-    "sqlalchemy>=2.0.40",
-]
+interpret_from_json = "hla_algorithm.interpret_from_json:main"
+update_alleles = "hla_algorithm.update_alleles:main"
+update_frequency_file = "hla_algorithm.update_frequency_file:main"
 
 [tool.hatch.version]
 source = "uv-dynamic-versioning"
 
 [tool.hatch.build]
 include = [
-  "src/easyhla/__about__.py",
-  "src/easyhla/__init__.py",
-  "src/easyhla/__main__.py",
-  "src/easyhla/easyhla.py",
-  "src/easyhla/interpret_from_json_lib.py",
-  "src/easyhla/interpret_from_json.py",
-  "src/easyhla/models.py",
-  "src/easyhla/py.typed",
-  "src/easyhla/update_alleles.py",
-  "src/easyhla/update_frequency_file_lib.py",
-  "src/easyhla/update_frequency_file.py",
-  "src/easyhla/utils.py",
-  "src/easyhla/default_data/hla_standards.yaml",
-  "src/easyhla/default_data/hla_frequencies.csv",
+  "src/hla_algorithm/_version.py",
+  "src/hla_algorithm/__init__.py",
+  "src/hla_algorithm/__main__.py",
+  "src/hla_algorithm/hla_algorithm.py",
+  "src/hla_algorithm/interpret_from_json_lib.py",
+  "src/hla_algorithm/interpret_from_json.py",
+  "src/hla_algorithm/models.py",
+  "src/hla_algorithm/py.typed",
+  "src/hla_algorithm/update_alleles.py",
+  "src/hla_algorithm/update_frequency_file_lib.py",
+  "src/hla_algorithm/update_frequency_file.py",
+  "src/hla_algorithm/utils.py",
+  "src/hla_algorithm/default_data/hla_standards.yaml",
+  "src/hla_algorithm/default_data/hla_frequencies.csv",
 ]
 exclude = [
   "tests",
@@ -101,10 +89,10 @@ skip-excluded-dirs = true
 directory = "output"
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/easyhla"]
+packages = ["src/hla_algorithm"]
 
 [tool.hatch.build.hooks.version]
-path = "src/easyhla/_version.py"
+path = "src/hla_algorithm/_version.py"
 template = '''
 __version__ = "{version}"
 '''
@@ -132,15 +120,13 @@ branch = true
 parallel = true
 source = ["src"]
 omit = [
-  "src/easyhla/__init__.py",
-  "src/easyhla/__about__.py",
-  "src/easyhla/__main__.py",
+  "src/hla_algorithm/__init__.py",
+  "src/hla_algorithm/_version.py",
+  "src/hla_algorithm/__main__.py",
   "tests/__init__.py",
-  "src/easyhla/bblab.py",
-  "src/easyhla/clinical_hla.py",
-  "src/easyhla/interpret_from_json.py",
-  "src/easyhla/update_alleles.py",
-  "src/easyhla/update_frequency_file.py",
+  "src/hla_algorithm/interpret_from_json.py",
+  "src/hla_algorithm/update_alleles.py",
+  "src/hla_algorithm/update_frequency_file.py",
   "src/scripts/*.py",
 ]
 

pyproject.toml

@@ -0,0 +1 @@
+*.gem

ruby/.gitignore

@@ -0,0 +1,19 @@
+Gem::Specification.new do |s|
+  s.name = "hla_algorithm"
+  s.version = ENV['HLA_ALGORITHM_VERSION'] || '0.0.0'
+  s.summary = "Ruby wrapper for the Python-based BC-CfE HLA interpretation algorithm"
+  s.files = ['lib/hla_algorithm.rb']
+  s.authors = [
+    "Brian Wynhoven",
+    "Chanson Brumme",
+    "Conan Woods",
+    "Rosemary McCloskey",
+    "David Rickett",
+    "Richard Liang"
+  ]
+  # Associate this gem with a GitHub repo; this allows the gems to be
+  # automatically associated with the repo when pushed to GitHub Packages.
+  s.metadata = {
+    "github_repo" => "ssh://github.com/cfe-lab/hla_algorithm"
+  }
+end

ruby/hla_algorithm.gemspec

@@ -56,8 +56,8 @@ def analyze(seqs, locus='B')
       "seq1" => seqs[0],
       "seq2" => seqs[1],
       "locus" => locus,
-      "hla_std_path" => File.expand_path(@hla_std_path),
-      "hla_freq_path" => File.expand_path(@hla_freq_path)
+      "hla_std_path" => nil,
+      "hla_freq_path" => nil
     }
 
     if (!@hla_std_path.nil?)