Feature/prioritise X over Y

.devcontainer/devcontainer.json

@@ -0,0 +1,37 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+	"name": "Python 3 + bcftools",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/python:3.10-bullseye",
+	"features": {
+		"ghcr.io/jungaretti/features/make:1": {}
+	},
+	"containerEnv": {
+		"PIP_DISABLE_PIP_VERSION_CHECK": "1",
+		"FASTA":"tests/fixtures/Homo_sapiens.GRCh38.dna.chromosome.X.Y.fa",
+		"REFGENE":"tests/fixtures/genes.refGene"
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	"forwardPorts": [9001],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "bash .devcontainer/setup_python.sh; bash .devcontainer/setup_dependencies.sh",
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"alexkrechik.cucumberautocomplete"
+			]
+		}
+	}
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.devcontainer/setup_dependencies.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+set -e
+
+BCFTOOLS_VERSION="1.18"
+
+sudo apt-get update
+sudo apt-get install -y wget build-essential bzip2 libz-dev liblzma-dev libbz2-dev libcurl4-openssl-dev
+
+CURRENT_DIR=`pwd`
+
+# Install bcftools
+wget -q https://github.com/samtools/bcftools/releases/download/$BCFTOOLS_VERSION/bcftools-$BCFTOOLS_VERSION.tar.bz2
+tar -vxjf bcftools-$BCFTOOLS_VERSION.tar.bz2
+cd bcftools-$BCFTOOLS_VERSION
+sudo make install
+cd $CURRENT_DIR
+rm -f bcftools-$BCFTOOLS_VERSION.tar.bz2
+rm -rf bcftools-$BCFTOOLS_VERSION
+
+# Install vcf_validator_linux
+wget -q https://github.com/EBIvariation/vcf-validator/releases/download/v0.9.5/vcf_validator_linux
+chmod +x vcf_validator_linux
+sudo mv vcf_validator_linux /usr/local/bin

.devcontainer/setup_python.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+set -e
+
+pip3 install --user -r requirements.txt
+pip3 install --user -r requirements-dev.txt

.dockerignore

@@ -0,0 +1,52 @@
+*.py[cod]
+
+# Emacs files
+*~
+*#
+
+# FASTA files
+*.fa.seqlen
+*.fa.pureseq
+*.fa.fai
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+.venv
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+.idea
+
+dist
+.git
+.devcontainer
+
+# Ignore generated files
+**/*.pyc

.github/workflows/publish_to_dockerhub.yml

@@ -0,0 +1,60 @@
+name: publish_to_dockerhub
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - master
+
+jobs:
+
+  publish_to_dockerhub:
+    runs-on: ubuntu-latest
+
+    environment:
+      name: dev
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Download refGene (sample dataset for tests)
+      run: ./download_refGene.sh -hg38_sample
+
+    - name: Run tests
+      run: ./run-tests.sh
+
+    - name: Cleanup
+      run: |
+        echo "Removing test fixtures"
+        rm -f tests/fixtures/Homo_sapiens.GRCh38.dna.chromosome.X.fa*
+        rm -f tests/fixtures/genes.refGene
+        rm -f tests/fixtures/LRG_RefSeqGene
+
+    - name: Download refGene
+      run: ./download_refGene.sh -hg38
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v2
+      with:
+        username: ${{ vars.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Docker meta
+      id: meta
+      uses: docker/metadata-action@v4
+      with:
+        images:  ${{ vars.DOCKERHUB_USERNAME }}/hgvs
+        tags: |
+          type=ref,event=branch
+          type=ref,event=pr
+          type=semver,pattern={{version}}
+          type=semver,pattern={{major}}.{{minor}}
+          type=sha
+
+    - name: Build and push
+      uses: docker/build-push-action@v4
+      with:
+        context: .
+        push: true
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}

.github/workflows/pull_request.yml

@@ -0,0 +1,23 @@
+name: pull_request
+
+on:
+  pull_request:
+    branches:
+      - master
+
+jobs:
+
+  pull_request:
+    runs-on: ubuntu-latest
+
+    environment:
+      name: dev
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Download refGene (sample dataset for tests)
+      run: ./download_refGene.sh -hg38_sample
+
+    - name: Run Tests
+      run: ./run-tests.sh

.gitignore

@@ -43,3 +43,14 @@ nosetests.xml
 .project
 .pydevproject
 .idea
+
+assemblies
+reference
+**/genes.refGene
+**/LRG_RefSeqGene
+tests/fixtures/*.fa**
+
+**/.DS_Store
+/bcftools*
+/tests/fixtures/hgvs_normalised/vcf_validator_linux
+*.vcf

.vscode/launch.json

@@ -0,0 +1,42 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: FastAPI",
+            "type": "python",
+            "request": "launch",
+            "module": "uvicorn",
+            "env": {
+                "FASTA": "assemblies/Homo_sapiens.GRCh38.dna.primary_assembly.fa",
+                "REFGENE": "reference/genes.refGene"
+            },
+            "args": [
+                "pyhgvs.api:app",
+                "--port", "9001",
+                "--reload"
+            ],
+            "jinja": true,
+            "justMyCode": true
+        },
+        {
+            "name": "Python: FastAPI - chrX",
+            "type": "python",
+            "request": "launch",
+            "module": "uvicorn",
+            "env": {
+                "FASTA": "tests/fixtures/Homo_sapiens.GRCh38.dna.chromosome.X.Y.fa",
+                "REFGENE": "tests/fixtures/genes.refGene"
+            },
+            "args": [
+                "pyhgvs.api:app",
+                "--port", "9001",
+                "--reload"
+            ],
+            "jinja": true,
+            "justMyCode": true
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

Dockerfile

@@ -0,0 +1,30 @@
+#################################################################################
+# STAGE - BUILD
+#################################################################################
+FROM python:3.10-slim as build
+
+# Keeps Python from generating .pyc files in the container
+ENV PYTHONDONTWRITEBYTECODE=1
+# Turns off buffering for easier container logging
+ENV PYTHONUNBUFFERED=1
+
+WORKDIR /app
+COPY requirements.txt .
+RUN python -m pip install --no-cache-dir --disable-pip-version-check -r requirements.txt
+COPY . /app
+
+#################################################################################
+# STAGE - TESTS
+#################################################################################
+FROM build as tests
+RUN python -m pip install --no-cache-dir --disable-pip-version-check -r requirements-dev.txt
+
+#################################################################################
+# STAGE - RUNTIME
+#################################################################################
+FROM python:3.10-slim AS runtime
+ENV PYTHONUNBUFFERED=1
+WORKDIR /app
+COPY --from=build /app /app
+COPY --from=build /usr/local /usr/local
+CMD ["uvicorn", "pyhgvs.api:app", "--host", "0.0.0.0", "--port", "8002"]

Makefile

@@ -1,32 +1,10 @@
-#! /usr/bin/make
-
 PACKAGE_NAME=pyhgvs
-SCRIPTS=bin/hgvs
-TEST_OUTPUT?=nosetests.xml
-
-VENV_DIR?=.venv
-VENV_ACTIVATE=$(VENV_DIR)/bin/activate
-WITH_VENV=. $(VENV_ACTIVATE);
-
-default:
-	python setup.py check build
-
-.PHONY: setup clean teardown venv lint test gitlint
 
-setup: venv
+default: package
 
-venv: $(VENV_ACTIVATE)
-
-$(VENV_DIR)/bin/activate: requirements-dev.txt
-	test -d $(VENV_DIR) || virtualenv --python=python2.7 --system-site-packages $(VENV_DIR)
-	$(WITH_VENV) pip install -r requirements-dev.txt
-	touch $(VENV_DIR)/bin/activate
-
-teardown:
-	rm -rf $(VENV_DIR)/
+.PHONY: clean lint test
 
 clean:
-	python setup.py clean
 	rm -rf build/
 	rm -rf dist/
 	rm -rf *.egg*/
@@ -35,11 +13,8 @@ clean:
 	rm -f $(TEST_OUTPUT)
 	find $(PACKAGE_NAME) -type f -name '*.pyc' -delete
 
-lint: venv
-	$(WITH_VENV) flake8 --jobs=auto $(PACKAGE_NAME)/ $(SCRIPTS)
-
-test: venv
-	$(WITH_VENV) nosetests --verbosity=2 --with-xunit --xunit-file=$(TEST_OUTPUT)
+lint:
+	flake8 --jobs=auto $(PACKAGE_NAME)/ $(SCRIPTS)
 
 package:
-	python setup.py sdist
+	python3 -m build