/
utils.py
775 lines (640 loc) · 29.5 KB
/
utils.py
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#!/usr/bin/env python
"""
Common utility functions for the nf-core python package.
"""
import nf_core
from distutils import version
import datetime
import errno
import git
import hashlib
import json
import logging
import mimetypes
import os
import prompt_toolkit
import questionary
import re
import requests
import requests_cache
import shlex
import subprocess
import sys
import time
import yaml
from rich.live import Live
from rich.spinner import Spinner
log = logging.getLogger(__name__)
# Custom style for questionary
nfcore_question_style = prompt_toolkit.styles.Style(
[
("qmark", "fg:ansiblue bold"), # token in front of the question
("question", "bold"), # question text
("answer", "fg:ansigreen nobold bg:"), # submitted answer text behind the question
("pointer", "fg:ansiyellow bold"), # pointer used in select and checkbox prompts
("highlighted", "fg:ansiblue bold"), # pointed-at choice in select and checkbox prompts
("selected", "fg:ansiyellow noreverse bold"), # style for a selected item of a checkbox
("separator", "fg:ansiblack"), # separator in lists
("instruction", ""), # user instructions for select, rawselect, checkbox
("text", ""), # plain text
("disabled", "fg:gray italic"), # disabled choices for select and checkbox prompts
("choice-default", "fg:ansiblack"),
("choice-default-changed", "fg:ansiyellow"),
("choice-required", "fg:ansired"),
]
)
def check_if_outdated(current_version=None, remote_version=None, source_url="https://nf-co.re/tools_version"):
"""
Check if the current version of nf-core is outdated
"""
# Exit immediately if disabled via ENV var
if os.environ.get("NFCORE_NO_VERSION_CHECK", False):
return True
# Set and clean up the current version string
if current_version == None:
current_version = nf_core.__version__
current_version = re.sub("[^0-9\.]", "", current_version)
# Build the URL to check against
source_url = os.environ.get("NFCORE_VERSION_URL", source_url)
source_url = "{}?v={}".format(source_url, current_version)
# Fetch and clean up the remote version
if remote_version == None:
response = requests.get(source_url, timeout=3)
remote_version = re.sub("[^0-9\.]", "", response.text)
# Check if we have an available update
is_outdated = version.StrictVersion(remote_version) > version.StrictVersion(current_version)
return (is_outdated, current_version, remote_version)
def rich_force_colors():
"""
Check if any environment variables are set to force Rich to use coloured output
"""
if os.getenv("GITHUB_ACTIONS") or os.getenv("FORCE_COLOR") or os.getenv("PY_COLORS"):
return True
return None
def github_api_auto_auth():
try:
with open(os.path.join(os.path.expanduser("~/.config/gh/hosts.yml")), "r") as fh:
auth = yaml.safe_load(fh)
log.debug("Auto-authenticating GitHub API as '@{}'".format(auth["github.com"]["user"]))
return requests.auth.HTTPBasicAuth(auth["github.com"]["user"], auth["github.com"]["oauth_token"])
except Exception as e:
log.debug(f"Couldn't auto-auth for GitHub: [red]{e}")
return None
class Pipeline(object):
"""Object to hold information about a local pipeline.
Args:
path (str): The path to the nf-core pipeline directory.
Attributes:
conda_config (dict): The parsed conda configuration file content (``environment.yml``).
conda_package_info (dict): The conda package(s) information, based on the API requests to Anaconda cloud.
nf_config (dict): The Nextflow pipeline configuration file content.
files (list): A list of files found during the linting process.
git_sha (str): The git sha for the repo commit / current GitHub pull-request (`$GITHUB_PR_COMMIT`)
minNextflowVersion (str): The minimum required Nextflow version to run the pipeline.
wf_path (str): Path to the pipeline directory.
pipeline_name (str): The pipeline name, without the `nf-core` tag, for example `hlatyping`.
schema_obj (obj): A :class:`PipelineSchema` object
"""
def __init__(self, wf_path):
"""Initialise pipeline object"""
self.conda_config = {}
self.conda_package_info = {}
self.nf_config = {}
self.files = []
self.git_sha = None
self.minNextflowVersion = None
self.wf_path = wf_path
self.pipeline_name = None
self.schema_obj = None
try:
repo = git.Repo(self.wf_path)
self.git_sha = repo.head.object.hexsha
except:
log.debug("Could not find git hash for pipeline: {}".format(self.wf_path))
# Overwrite if we have the last commit from the PR - otherwise we get a merge commit hash
if os.environ.get("GITHUB_PR_COMMIT", "") != "":
self.git_sha = os.environ["GITHUB_PR_COMMIT"]
def _load(self):
"""Run core load functions"""
self._list_files()
self._load_pipeline_config()
self._load_conda_environment()
def _list_files(self):
"""Get a list of all files in the pipeline"""
try:
# First, try to get the list of files using git
git_ls_files = subprocess.check_output(["git", "ls-files"], cwd=self.wf_path).splitlines()
self.files = []
for fn in git_ls_files:
full_fn = os.path.join(self.wf_path, fn.decode("utf-8"))
if os.path.isfile(full_fn):
self.files.append(full_fn)
else:
log.debug("`git ls-files` returned '{}' but could not open it!".format(full_fn))
except subprocess.CalledProcessError as e:
# Failed, so probably not initialised as a git repository - just a list of all files
log.debug("Couldn't call 'git ls-files': {}".format(e))
self.files = []
for subdir, dirs, files in os.walk(self.wf_path):
for fn in files:
self.files.append(os.path.join(subdir, fn))
def _load_pipeline_config(self):
"""Get the nextflow config for this pipeline
Once loaded, set a few convienence reference class attributes
"""
self.nf_config = fetch_wf_config(self.wf_path)
self.pipeline_name = self.nf_config.get("manifest.name", "").strip("'").replace("nf-core/", "")
nextflowVersionMatch = re.search(r"[0-9\.]+(-edge)?", self.nf_config.get("manifest.nextflowVersion", ""))
if nextflowVersionMatch:
self.minNextflowVersion = nextflowVersionMatch.group(0)
def _load_conda_environment(self):
"""Try to load the pipeline environment.yml file, if it exists"""
try:
with open(os.path.join(self.wf_path, "environment.yml"), "r") as fh:
self.conda_config = yaml.safe_load(fh)
except FileNotFoundError:
log.debug("No conda `environment.yml` file found.")
def _fp(self, fn):
"""Convenience function to get full path to a file in the pipeline"""
return os.path.join(self.wf_path, fn)
def is_pipeline_directory(wf_path):
"""
Checks if the specified directory have the minimum required files
('main.nf', 'nextflow.config') for a pipeline directory
Args:
wf_path (str): The directory to be inspected
Raises:
UserWarning: If one of the files are missing
"""
for fn in ["main.nf", "nextflow.config"]:
path = os.path.join(wf_path, fn)
if not os.path.isfile(path):
raise UserWarning(f"'{wf_path}' is not a pipeline - '{fn}' is missing")
def fetch_wf_config(wf_path):
"""Uses Nextflow to retrieve the the configuration variables
from a Nextflow workflow.
Args:
wf_path (str): Nextflow workflow file system path.
Returns:
dict: Workflow configuration settings.
"""
config = dict()
cache_fn = None
cache_basedir = None
cache_path = None
# Nextflow home directory - use env var if set, or default to ~/.nextflow
nxf_home = os.environ.get("NXF_HOME", os.path.join(os.getenv("HOME"), ".nextflow"))
# Build a cache directory if we can
if os.path.isdir(nxf_home):
cache_basedir = os.path.join(nxf_home, "nf-core")
if not os.path.isdir(cache_basedir):
os.mkdir(cache_basedir)
# If we're given a workflow object with a commit, see if we have a cached copy
cache_fn = None
# Make a filename based on file contents
concat_hash = ""
for fn in ["nextflow.config", "main.nf"]:
try:
with open(os.path.join(wf_path, fn), "rb") as fh:
concat_hash += hashlib.sha256(fh.read()).hexdigest()
except FileNotFoundError as e:
pass
# Hash the hash
if len(concat_hash) > 0:
bighash = hashlib.sha256(concat_hash.encode("utf-8")).hexdigest()
cache_fn = "wf-config-cache-{}.json".format(bighash[:25])
if cache_basedir and cache_fn:
cache_path = os.path.join(cache_basedir, cache_fn)
if os.path.isfile(cache_path):
log.debug("Found a config cache, loading: {}".format(cache_path))
with open(cache_path, "r") as fh:
config = json.load(fh)
return config
log.debug("No config cache found")
# Call `nextflow config`
nfconfig_raw = nextflow_cmd(f"nextflow config -flat {wf_path}")
for l in nfconfig_raw.splitlines():
ul = l.decode("utf-8")
try:
k, v = ul.split(" = ", 1)
config[k] = v
except ValueError:
log.debug("Couldn't find key=value config pair:\n {}".format(ul))
# Scrape main.nf for additional parameter declarations
# Values in this file are likely to be complex, so don't both trying to capture them. Just get the param name.
try:
main_nf = os.path.join(wf_path, "main.nf")
with open(main_nf, "r") as fh:
for l in fh:
match = re.match(r"^\s*(params\.[a-zA-Z0-9_]+)\s*=", l)
if match:
config[match.group(1)] = "false"
except FileNotFoundError as e:
log.debug("Could not open {} to look for parameter declarations - {}".format(main_nf, e))
# If we can, save a cached copy
if cache_path:
log.debug("Saving config cache: {}".format(cache_path))
with open(cache_path, "w") as fh:
json.dump(config, fh, indent=4)
return config
def nextflow_cmd(cmd):
"""Run a Nextflow command and capture the output. Handle errors nicely"""
try:
nf_proc = subprocess.run(shlex.split(cmd), stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
return nf_proc.stdout
except OSError as e:
if e.errno == errno.ENOENT:
raise AssertionError("It looks like Nextflow is not installed. It is required for most nf-core functions.")
except subprocess.CalledProcessError as e:
raise AssertionError(
f"Command '{cmd}' returned non-zero error code '{e.returncode}':\n[red]> {e.stderr.decode()}"
)
def setup_requests_cachedir():
"""Sets up local caching for faster remote HTTP requests.
Caching directory will be set up in the user's home directory under
a .nfcore_cache subdir.
"""
pyversion = ".".join(str(v) for v in sys.version_info[0:3])
cachedir = os.path.join(os.getenv("HOME"), os.path.join(".nfcore", "cache_" + pyversion))
try:
if not os.path.exists(cachedir):
os.makedirs(cachedir)
requests_cache.install_cache(
os.path.join(cachedir, "github_info"),
expire_after=datetime.timedelta(hours=1),
backend="sqlite",
)
except PermissionError:
pass
def wait_cli_function(poll_func, poll_every=20):
"""
Display a command-line spinner while calling a function repeatedly.
Keep waiting until that function returns True
Arguments:
poll_func (function): Function to call
poll_every (int): How many tenths of a second to wait between function calls. Default: 20.
Returns:
None. Just sits in an infite loop until the function returns True.
"""
try:
spinner = Spinner("dots2", "Use ctrl+c to stop waiting and force exit.")
with Live(spinner, refresh_per_second=20) as live:
while True:
if poll_func():
break
time.sleep(2)
except KeyboardInterrupt:
raise AssertionError("Cancelled!")
def poll_nfcore_web_api(api_url, post_data=None):
"""
Poll the nf-core website API
Takes argument api_url for URL
Expects API reponse to be valid JSON and contain a top-level 'status' key.
"""
# Run without requests_cache so that we get the updated statuses
with requests_cache.disabled():
try:
if post_data is None:
response = requests.get(api_url, headers={"Cache-Control": "no-cache"})
else:
response = requests.post(url=api_url, data=post_data)
except (requests.exceptions.Timeout):
raise AssertionError("URL timed out: {}".format(api_url))
except (requests.exceptions.ConnectionError):
raise AssertionError("Could not connect to URL: {}".format(api_url))
else:
if response.status_code != 200:
log.debug("Response content:\n{}".format(response.content))
raise AssertionError(
"Could not access remote API results: {} (HTML {} Error)".format(api_url, response.status_code)
)
else:
try:
web_response = json.loads(response.content)
assert "status" in web_response
except (json.decoder.JSONDecodeError, AssertionError, TypeError) as e:
log.debug("Response content:\n{}".format(response.content))
raise AssertionError(
"nf-core website API results response not recognised: {}\n See verbose log for full response".format(
api_url
)
)
else:
return web_response
def anaconda_package(dep, dep_channels=["conda-forge", "bioconda", "defaults"]):
"""Query conda package information.
Sends a HTTP GET request to the Anaconda remote API.
Args:
dep (str): A conda package name.
dep_channels (list): list of conda channels to use
Raises:
A LookupError, if the connection fails or times out or gives an unexpected status code
A ValueError, if the package name can not be found (404)
"""
# Check if each dependency is the latest available version
if "=" in dep:
depname, depver = dep.split("=", 1)
else:
depname = dep
# 'defaults' isn't actually a channel name. See https://docs.anaconda.com/anaconda/user-guide/tasks/using-repositories/
if "defaults" in dep_channels:
dep_channels.remove("defaults")
dep_channels.extend(["main", "anaconda", "r", "free", "archive", "anaconda-extras"])
if "::" in depname:
dep_channels = [depname.split("::")[0]]
depname = depname.split("::")[1]
for ch in dep_channels:
anaconda_api_url = "https://api.anaconda.org/package/{}/{}".format(ch, depname)
try:
response = requests.get(anaconda_api_url, timeout=10)
except (requests.exceptions.Timeout):
raise LookupError("Anaconda API timed out: {}".format(anaconda_api_url))
except (requests.exceptions.ConnectionError):
raise LookupError("Could not connect to Anaconda API")
else:
if response.status_code == 200:
return response.json()
elif response.status_code != 404:
raise LookupError(
"Anaconda API returned unexpected response code `{}` for: {}\n{}".format(
response.status_code, anaconda_api_url, response
)
)
elif response.status_code == 404:
log.debug("Could not find `{}` in conda channel `{}`".format(dep, ch))
else:
# We have looped through each channel and had a 404 response code on everything
raise ValueError(f"Could not find Conda dependency using the Anaconda API: '{dep}'")
def parse_anaconda_licence(anaconda_response, version=None):
"""Given a response from the anaconda API using anaconda_package, parse the software licences.
Returns: Set of licence types
"""
licences = set()
# Licence for each version
for f in anaconda_response["files"]:
if not version or version == f.get("version"):
try:
licences.add(f["attrs"]["license"])
except KeyError:
pass
# Main licence field
if len(list(licences)) == 0 and isinstance(anaconda_response["license"], str):
licences.add(anaconda_response["license"])
# Clean up / standardise licence names
clean_licences = []
for l in licences:
l = re.sub(r"GNU General Public License v\d \(([^\)]+)\)", r"\1", l)
l = re.sub(r"GNU GENERAL PUBLIC LICENSE", "GPL", l, flags=re.IGNORECASE)
l = l.replace("GPL-", "GPLv")
l = re.sub(r"GPL\s*([\d\.]+)", r"GPL v\1", l) # Add v prefix to GPL version if none found
l = re.sub(r"GPL\s*v(\d).0", r"GPL v\1", l) # Remove superflous .0 from GPL version
l = re.sub(r"GPL \(([^\)]+)\)", r"GPL \1", l)
l = re.sub(r"GPL\s*v", "GPL v", l) # Normalise whitespace to one space between GPL and v
l = re.sub(r"\s*(>=?)\s*(\d)", r" \1\2", l) # Normalise whitespace around >= GPL versions
l = l.replace("Clause", "clause") # BSD capitilisation
l = re.sub(r"-only$", "", l) # Remove superflous GPL "only" version suffixes
clean_licences.append(l)
return clean_licences
def pip_package(dep):
"""Query PyPI package information.
Sends a HTTP GET request to the PyPI remote API.
Args:
dep (str): A PyPI package name.
Raises:
A LookupError, if the connection fails or times out
A ValueError, if the package name can not be found
"""
pip_depname, pip_depver = dep.split("=", 1)
pip_api_url = "https://pypi.python.org/pypi/{}/json".format(pip_depname)
try:
response = requests.get(pip_api_url, timeout=10)
except (requests.exceptions.Timeout):
raise LookupError("PyPI API timed out: {}".format(pip_api_url))
except (requests.exceptions.ConnectionError):
raise LookupError("PyPI API Connection error: {}".format(pip_api_url))
else:
if response.status_code == 200:
return response.json()
else:
raise ValueError("Could not find pip dependency using the PyPI API: `{}`".format(dep))
def get_biocontainer_tag(package, version):
"""
Given a bioconda package and version, looks for Docker and Singularity containers
using the biocontaineres API, e.g.:
https://api.biocontainers.pro/ga4gh/trs/v2/tools/{tool}/versions/{tool}-{version}
Returns the most recent container versions by default.
Args:
package (str): A bioconda package name.
version (str): Version of the bioconda package
Raises:
A LookupError, if the connection fails or times out or gives an unexpected status code
A ValueError, if the package name can not be found (404)
"""
biocontainers_api_url = f"https://api.biocontainers.pro/ga4gh/trs/v2/tools/{package}/versions/{package}-{version}"
def get_tag_date(tag_date):
"""
Format a date given by the biocontainers API
Given format: '2021-03-25T08:53:00Z'
"""
return datetime.datetime.strptime(tag_date, "%Y-%m-%dT%H:%M:%SZ")
try:
response = requests.get(biocontainers_api_url)
except requests.exceptions.ConnectionError:
raise LookupError("Could not connect to biocontainers.pro API")
else:
if response.status_code == 200:
try:
images = response.json()["images"]
singularity_image = None
docker_image = None
for img in images:
# Get most recent Docker and Singularity image
if img["image_type"] == "Docker":
modification_date = get_tag_date(img["updated"])
if not docker_image or modification_date > get_tag_date(docker_image["updated"]):
docker_image = img
if img["image_type"] == "Singularity":
modification_date = get_tag_date(img["updated"])
if not singularity_image or modification_date > get_tag_date(singularity_image["updated"]):
singularity_image = img
return docker_image["image_name"], singularity_image["image_name"]
except TypeError:
raise LookupError(f"Could not find docker or singularity container for {package}")
elif response.status_code != 404:
raise LookupError(f"Unexpected response code `{response.status_code}` for {biocontainers_api_url}")
elif response.status_code == 404:
raise ValueError(f"Could not find `{package}` on api.biocontainers.pro")
def custom_yaml_dumper():
"""Overwrite default PyYAML output to make Prettier YAML linting happy"""
class CustomDumper(yaml.Dumper):
def represent_dict_preserve_order(self, data):
"""Add custom dumper class to prevent overwriting the global state
This prevents yaml from changing the output order
See https://stackoverflow.com/a/52621703/1497385
"""
return self.represent_dict(data.items())
def increase_indent(self, flow=False, *args, **kwargs):
"""Indent YAML lists so that YAML validates with Prettier
See https://github.com/yaml/pyyaml/issues/234#issuecomment-765894586
"""
return super().increase_indent(flow=flow, indentless=False)
# HACK: insert blank lines between top-level objects
# inspired by https://stackoverflow.com/a/44284819/3786245
# and https://github.com/yaml/pyyaml/issues/127
def write_line_break(self, data=None):
super().write_line_break(data)
if len(self.indents) == 1:
super().write_line_break()
CustomDumper.add_representer(dict, CustomDumper.represent_dict_preserve_order)
return CustomDumper
def is_file_binary(path):
"""Check file path to see if it is a binary file"""
binary_ftypes = ["image", "application/java-archive", "application/x-java-archive"]
binary_extensions = [".jpeg", ".jpg", ".png", ".zip", ".gz", ".jar", ".tar"]
# Check common file extensions
filename, file_extension = os.path.splitext(path)
if file_extension in binary_extensions:
return True
# Try to detect binary files
(ftype, encoding) = mimetypes.guess_type(path, strict=False)
if encoding is not None or (ftype is not None and any([ftype.startswith(ft) for ft in binary_ftypes])):
return True
def prompt_remote_pipeline_name(wfs):
"""Prompt for the pipeline name with questionary
Args:
wfs: A nf_core.list.Workflows() object, where get_remote_workflows() has been called.
Returns:
pipeline (str): GitHub repo - username/repo
Raises:
AssertionError, if pipeline cannot be found
"""
pipeline = questionary.autocomplete(
"Pipeline name:",
choices=[wf.name for wf in wfs.remote_workflows],
style=nfcore_question_style,
).unsafe_ask()
# Check nf-core repos
for wf in wfs.remote_workflows:
if wf.full_name == pipeline or wf.name == pipeline:
return wf.full_name
# Non nf-core repo on GitHub
else:
if pipeline.count("/") == 1:
try:
gh_response = requests.get(f"https://api.github.com/repos/{pipeline}")
assert gh_response.json().get("message") != "Not Found"
except AssertionError:
pass
else:
return pipeline
log.info("Available nf-core pipelines: '{}'".format("', '".join([w.name for w in wfs.remote_workflows])))
raise AssertionError(f"Not able to find pipeline '{pipeline}'")
def prompt_pipeline_release_branch(wf_releases, wf_branches):
"""Prompt for pipeline release / branch
Args:
wf_releases (array): Array of repo releases as returned by the GitHub API
wf_branches (array): Array of repo branches, as returned by the GitHub API
Returns:
choice (str): Selected release / branch name
"""
# Prompt user for release tag
choices = []
# Releases
if len(wf_releases) > 0:
for tag in map(lambda release: release.get("tag_name"), wf_releases):
tag_display = [("fg:ansiblue", f"{tag} "), ("class:choice-default", "[release]")]
choices.append(questionary.Choice(title=tag_display, value=tag))
# Branches
for branch in wf_branches.keys():
branch_display = [("fg:ansiyellow", f"{branch} "), ("class:choice-default", "[branch]")]
choices.append(questionary.Choice(title=branch_display, value=branch))
if len(choices) == 0:
return False
return questionary.select("Select release / branch:", choices=choices, style=nfcore_question_style).unsafe_ask()
def get_repo_releases_branches(pipeline, wfs):
"""Fetches details of a nf-core workflow to download.
Args:
pipeline (str): GitHub repo username/repo
wfs: A nf_core.list.Workflows() object, where get_remote_workflows() has been called.
Returns:
wf_releases, wf_branches (tuple): Array of releases, Array of branches
Raises:
LockupError, if the pipeline can not be found.
"""
wf_releases = []
wf_branches = {}
# Repo is a nf-core pipeline
for wf in wfs.remote_workflows:
if wf.full_name == pipeline or wf.name == pipeline:
# Set to full name just in case it didn't have the nf-core/ prefix
pipeline = wf.full_name
# Store releases and stop loop
wf_releases = list(sorted(wf.releases, key=lambda k: k.get("published_at_timestamp", 0), reverse=True))
break
# Arbitrary GitHub repo
else:
if pipeline.count("/") == 1:
# Looks like a GitHub address - try working with this repo
log.debug(
f"Pipeline '{pipeline}' not in nf-core, but looks like a GitHub address - fetching releases from API"
)
# Get releases from GitHub API
rel_r = requests.get(f"https://api.github.com/repos/{pipeline}/releases")
# Check that this repo existed
try:
assert rel_r.json().get("message") != "Not Found"
except AssertionError:
raise AssertionError(f"Not able to find pipeline '{pipeline}'")
except AttributeError:
# When things are working we get a list, which doesn't work with .get()
wf_releases = list(sorted(rel_r.json(), key=lambda k: k.get("published_at_timestamp", 0), reverse=True))
# Get release tag commit hashes
if len(wf_releases) > 0:
# Get commit hash information for each release
tags_r = requests.get(f"https://api.github.com/repos/{pipeline}/tags")
for tag in tags_r.json():
for release in wf_releases:
if tag["name"] == release["tag_name"]:
release["tag_sha"] = tag["commit"]["sha"]
else:
log.info("Available nf-core pipelines: '{}'".format("', '".join([w.name for w in wfs.remote_workflows])))
raise AssertionError(f"Not able to find pipeline '{pipeline}'")
# Get branch information from github api - should be no need to check if the repo exists again
branch_response = requests.get(f"https://api.github.com/repos/{pipeline}/branches")
for branch in branch_response.json():
if (
branch["name"] != "TEMPLATE"
and branch["name"] != "initial_commit"
and not branch["name"].startswith("nf-core-template-merge")
):
wf_branches[branch["name"]] = branch["commit"]["sha"]
# Return pipeline again in case we added the nf-core/ prefix
return pipeline, wf_releases, wf_branches
def load_tools_config(dir="."):
"""
Parse the nf-core.yml configuration file
Look for a file called either `.nf-core.yml` or `.nf-core.yaml`
Also looks for the deprecated file `.nf-core-lint.yml/yaml` and issues
a warning that this file will be deprecated in the future
Returns the loaded config dict or False, if the file couldn't be loaded
"""
tools_config = {}
config_fn = os.path.join(dir, ".nf-core.yml")
# Check if old config file is used
old_config_fn_yml = os.path.join(dir, ".nf-core-lint.yml")
old_config_fn_yaml = os.path.join(dir, ".nf-core-lint.yaml")
if os.path.isfile(old_config_fn_yml) or os.path.isfile(old_config_fn_yaml):
log.error(
f"Deprecated `nf-core-lint.yml` file found! The file will not be loaded. Please rename the file to `.nf-core.yml`."
)
return {}
if not os.path.isfile(config_fn):
config_fn = os.path.join(dir, ".nf-core.yaml")
# Load the YAML
try:
with open(config_fn, "r") as fh:
tools_config = yaml.safe_load(fh)
except FileNotFoundError:
log.debug(f"No tools config file found: {config_fn}")
return {}
return tools_config