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Merge pull request #356 from michellab/feature-web
Feature web (a.k.a. BioSimSpace 2023.0.0) [ci skip]
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
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| # Script that collects as much as it can from a failed conda build so that it can | ||
| # be stored as a GitHub Actions artifact for download and further debugging | ||
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| import os | ||
| import sys | ||
| import glob | ||
| import tarfile | ||
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| if "BUILD_DIR" not in os.environ: | ||
| try: | ||
| os.environ["BUILD_DIR"] = sys.argv[1] | ||
| except Exception: | ||
| print("You need to supply BUILD_DIR") | ||
| sys.exit(-1) | ||
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| build_dir = os.environ["BUILD_DIR"] | ||
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| # We want to bzip up the last 'sire-*' and all 'broken-*' directories in build_dir | ||
| work_dirs = glob.glob(os.path.join(build_dir, "biosimspace_*", "work", "build")) | ||
| broken_dirs = glob.glob(os.path.join(build_dir, "broke*")) | ||
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| if len(work_dirs) > 0: | ||
| work_dirs = [work_dirs[-1]] | ||
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| zipdirs = work_dirs + broken_dirs | ||
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| output_filename = os.path.join(build_dir, "failed.tar.bz2") | ||
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| print(f"Zipping up {zipdirs} to {output_filename}") | ||
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| def filter_function(tarinfo): | ||
| filename = tarinfo.name | ||
| #print(filename) | ||
| if filename.find('.git') != -1: | ||
| #print("excluded!") | ||
| return None | ||
| else: | ||
| return tarinfo | ||
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| with tarfile.open(output_filename, "w:bz2") as tar: | ||
| for dir in zipdirs: | ||
| tar.add(dir, arcname=os.path.basename(dir), filter=filter_function) | ||
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| print("Complete :-)") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
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| def parse_requirements(filename): | ||
| """Parse the requirements and return (in conda notation) | ||
| the requirements for this system | ||
| """ | ||
| try: | ||
| from pip_requirements_parser import RequirementsFile | ||
| except ImportError as e: | ||
| print("\n\n[ERROR] ** You need to install pip-requirements-parser") | ||
| print("Run `conda install pip-requirements-parser\n\n") | ||
| raise e | ||
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| from pkg_resources import evaluate_marker | ||
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| reqs = RequirementsFile.from_file(filename).to_dict()["requirements"] | ||
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| deps = {} | ||
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| for req in reqs: | ||
| name = req["name"] | ||
| specifier = req["specifier"] | ||
| marker = req["marker"] | ||
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| if len(specifier) == 0: | ||
| specifier = "" | ||
| else: | ||
| specifier = specifier[0] | ||
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| if marker is not None: | ||
| # check to see if this line fits this platform | ||
| include = evaluate_marker(marker) | ||
| else: | ||
| include = True | ||
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| if include: | ||
| deps[name] = specifier | ||
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| reqs = list(deps.keys()) | ||
| reqs.sort() | ||
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| result = [] | ||
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| for req in reqs: | ||
| result.append(f"{req}{deps[req]}") | ||
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| return result |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
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| import sys | ||
| import os | ||
| import subprocess | ||
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| script = os.path.abspath(sys.argv[0]) | ||
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| # we want to import the 'get_requirements' package from this directory | ||
| sys.path.insert(0, os.path.dirname(script)) | ||
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| from parse_requirements import parse_requirements | ||
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| # go up one directories to get the source directory | ||
| # (this script is in BioSimSpace/actions/) | ||
| srcdir = os.path.dirname(os.path.dirname(script)) | ||
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| condadir = os.path.join(srcdir, "recipes", "biosimspace") | ||
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| print(f"conda recipe in {condadir}") | ||
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| # Store the name of the recipe and template YAML files. | ||
| recipe = os.path.join(condadir, "meta.yaml") | ||
| template = os.path.join(condadir, "template.yaml") | ||
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| # Now parse all of the requirements | ||
| run_reqs = parse_requirements(os.path.join(srcdir, "requirements.txt")) | ||
| print(run_reqs) | ||
| build_reqs = parse_requirements(os.path.join(srcdir, "requirements_build.txt")) | ||
| print(build_reqs) | ||
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| def run_cmd(cmd): | ||
| p = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE) | ||
| return str(p.stdout.read().decode("utf-8")).lstrip().rstrip() | ||
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| gitdir = os.path.join(srcdir, ".git") | ||
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| # Get the BSS branch. | ||
| branch = run_cmd(f"git --git-dir={gitdir} --work-tree={srcdir} rev-parse --abbrev-ref HEAD") | ||
| print(branch) | ||
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| lines = open(template, "r").readlines() | ||
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| def dep_lines(deps): | ||
| lines = [] | ||
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| for dep in deps: | ||
| lines.append(f" - {dep}\n") | ||
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| return "".join(lines) | ||
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| run_reqs = dep_lines(run_reqs) | ||
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| if len(build_reqs) > 0: | ||
| build_reqs = f" build:\n{dep_lines(build_reqs)}" | ||
| else: | ||
| build_reqs = "" | ||
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| with open(recipe, "w") as FILE: | ||
| for line in lines: | ||
| if line.find("BSS_BUILD_REQUIREMENTS") != -1: | ||
| line = build_reqs | ||
| elif line.find("BSS_RUN_REQUIREMENTS") != -1: | ||
| line = run_reqs | ||
| else: | ||
| line = line.replace("BSS_BRANCH", branch) | ||
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| FILE.write(line) |
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