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import yaml
import subprocess
# we use this script to format the dependencies for the pyproject.toml and recipe.yml files
# Function to run a shell command and capture the output
def run_command(command):
result = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, text=True)
if result.returncode != 0:
print(f"Error running command: {command}\n{result.stderr}")
raise Exception(result.stderr)
return result.stdout
# Function to get the installed version of a package
def get_installed_version(package_name):
try:
output = run_command(f"micromamba list ^{package_name}$")
line = output.strip().split('\n')[4] # Skip the header lines
parts = line.split()
if len(parts) > 1:
return parts[1]
except Exception as e:
print(f"Could not find installed version for {package_name}: {e}")
return None
def get_installed_version_pip(package_name):
try:
output = run_command(f"pip show {package_name}")
line = output.strip().split('\n')[1] # Skip the first line
parts = line.split()
if len(parts) > 1:
return parts[1]
except Exception as e:
print(f"Could not find installed version for {package_name}: {e}")
return None
# Function to parse the environment.yml file and extract package information with versions
def parse_environment_file(env_file):
with open(env_file, 'r') as f:
env_data = yaml.safe_load(f)
conda_packages = []
pip_packages = []
for dep in env_data['dependencies']:
if isinstance(dep, str):
package_name = dep.split('=')[0].lower()
version = get_installed_version(package_name)
print(package_name, version)
if version:
conda_packages.append(f"{package_name}=={version}")
else:
conda_packages.append(package_name)
elif isinstance(dep, dict) and 'pip' in dep:
for pip_dep in dep['pip']:
package_name = pip_dep.split('==')[0]
version = get_installed_version_pip(package_name)
print(package_name, version)
if version:
pip_packages.append(f"{package_name}=={version}")
else:
pip_packages.append(pip_dep)
return conda_packages, pip_packages
# Function to generate the pyproject.toml
def generate_deps_list(conda_packages, pip_packages):
dependencies = conda_packages + pip_packages
deps_toml = [f"\"{d}\"" for d in dependencies]
deps_recipe = [" ==".join(d.split("==")) for d in dependencies]
# print(dependencies)
file_toml = "./deps_toml.txt"
file_recipe = "./deps_recipe.txt"
with open(file_toml, 'w') as f:
f.write(", ".join(deps_toml))
with open(file_recipe, 'w') as f:
f.write("\n".join([f"- {d}" for d in deps_recipe]))
print(f"Dependency files {file_toml} and {file_recipe} have been generated.")
if __name__ == "__main__":
original_env_file = 'environment.yaml'
# original_env_file = 'environment-cf.yaml'
conda_packages, pip_packages = parse_environment_file(original_env_file)
generate_deps_list(conda_packages, pip_packages)
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