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Makefile
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SHELL := /usr/bin/env bash
PYTHON_VERSION := 3.11.7
PYTHON_VERSION_CONDENSED := 311
PACKAGE_NAME := biosc1540-2024s
CONDA_NAME := $(PACKAGE_NAME)-dev
CONDA := conda run -n $(CONDA_NAME)
CONDA_LOCK_OPTIONS := -p linux-64 --channel conda-forge --channel nvidia --channel pytorch --channel bioconda
### ENVIRONMENT ###
# See https://github.com/pypa/pip/issues/7883#issuecomment-643319919
export PYTHON_KEYRING_BACKEND := keyring.backends.null.Keyring
.PHONY: conda-create
conda-create:
- conda deactivate
conda remove -y -n $(CONDA_NAME) --all
conda create -y -n $(CONDA_NAME)
$(CONDA) conda install -y -c conda-forge python=$(PYTHON_VERSION)
$(CONDA) conda install -y conda-lock
# Default packages that we always need.
.PHONY: conda-setup
conda-setup:
$(CONDA) conda install -y -c conda-forge poetry
$(CONDA) conda install -y -c conda-forge pre-commit
$(CONDA) conda install -y -c conda-forge tomli tomli-w
$(CONDA) conda install -y -c conda-forge conda-poetry-liaison
# Conda-only packages specific to this project.
.PHONY: conda-dependencies
conda-dependencies:
$(CONDA) conda install -y -c conda-forge nodejs
$(CONDA) conda install -y -c bioconda clustalw
$(CONDA) conda install -y -c bioconda salmon
$(CONDA) conda install -y -c conda-forge openmm
.PHONY: nodejs-dependencies
nodejs-dependencies:
$(CONDA) npm install markdownlint-cli2 --global
.PHONY: conda-lock
conda-lock:
- rm conda-lock.yml
$(CONDA) conda env export --from-history | grep -v "^prefix" > environment.yml
$(CONDA) conda-lock -f environment.yml $(CONDA_LOCK_OPTIONS)
rm environment.yml
$(CONDA) cpl-deps pyproject.toml --env_name $(CONDA_NAME)
$(CONDA) cpl-clean --env_name $(CONDA_NAME)
.PHONY: from-conda-lock
from-conda-lock:
$(CONDA) conda-lock install -n $(CONDA_NAME) conda-lock.yml
$(CONDA) cpl-clean --env_name $(CONDA_NAME)
.PHONY: pre-commit-install
pre-commit-install:
$(CONDA) pre-commit install
# Reads `pyproject.toml`, solves environment, then writes lock file.
.PHONY: poetry-lock
poetry-lock:
$(CONDA) poetry lock --no-interaction
.PHONY: install
install:
$(CONDA) poetry install --no-interaction --no-root
.PHONY: environment
environment: conda-create from-conda-lock pre-commit-install nodejs-dependencies install
.PHONY: locks
locks: conda-create conda-setup conda-dependencies conda-lock pre-commit-install poetry-lock nodejs-dependencies install
### FORMATTING ###
.PHONY: validate
validate:
$(CONDA) markdownlint-cli2-fix biosc1540/*
$(CONDA) pre-commit run --all-files
.PHONY: formatting
formatting:
- $(CONDA) isort --settings-path pyproject.toml ./
- $(CONDA) black --config pyproject.toml ./
### LINTING ###
.PHONY: check-codestyle
check-codestyle:
$(CONDA) isort --diff --check-only $(REPO_PATH)
$(CONDA) black --diff --check --config pyproject.toml $(REPO_PATH)
$(CONDA) pylint --recursive=y --rcfile pyproject.toml $(REPO_PATH)
.PHONY: lint
lint: check-codestyle
### CLEANING ###
.PHONY: pycache-remove
pycache-remove:
find . | grep -E "(__pycache__|\.pyc|\.pyo$$)" | xargs rm -rf
.PHONY: dsstore-remove
dsstore-remove:
find . | grep -E ".DS_Store" | xargs rm -rf
.PHONY: mypycache-remove
mypycache-remove:
find . | grep -E ".mypy_cache" | xargs rm -rf
.PHONY: ipynbcheckpoints-remove
ipynbcheckpoints-remove:
find . | grep -E ".ipynb_checkpoints" | xargs rm -rf
.PHONY: pytestcache-remove
pytestcache-remove:
find . | grep -E ".pytest_cache" | xargs rm -rf
.PHONY: build-remove
build-remove:
rm -rf build/
.PHONY: cleanup
cleanup: pycache-remove dsstore-remove mypycache-remove ipynbcheckpoints-remove pytestcache-remove
### MKDOCS ###
mkdocs_port := $(shell \
start_port=3000; \
max_attempts=100; \
for i in $$(seq 0 $$(($$max_attempts - 1))); do \
current_port=$$(($$start_port + i)); \
if ! lsof -i :$$current_port > /dev/null; then \
echo $$current_port; \
break; \
fi; \
if [ $$i -eq $$(($$max_attempts - 1)) ]; then \
echo "Error: Unable to find an available port after $$max_attempts attempts."; \
exit 1; \
fi; \
done \
)
.PHONY: serve
serve:
echo "Served at http://127.0.0.1:$(mkdocs_port)/"
$(CONDA) mkdocs serve -a localhost:$(mkdocs_port)
.PHONY: docs
docs:
$(CONDA) mkdocs build -d public/
.PHONY: open-docs
open-docs:
xdg-open public/index.html 2>/dev/null