wholecell.utils.filepath
filepath.py File and filename path utilities.
- wholecell.utils.filepath.git_branch()[source]
Return the source code git branch name, or the environment variable $IMAGE_GIT_BRANCH if there’s no git repo (in a Docker Image), or ‘–‘.
- wholecell.utils.filepath.git_hash()[source]
Return the source code git hash, or the environment variable $IMAGE_GIT_HASH if there’s no git repo (in a Docker Image), or else ‘–‘.
- wholecell.utils.filepath.iter_variants(variant_type, first_index, last_index)[source]
Generate Variant subdirs (index, name) over [first .. last] inclusive.
- wholecell.utils.filepath.makedirs(path, *paths)[source]
Join one or more path components, make that directory path (using the default mode 0o0777), and return the full path.
Raise FileExistsError if there’s a file (not a directory) with that path. No exception if the directory already exists.
- wholecell.utils.filepath.read_json_file(filename)[source]
Read and parse JSON file. This supports Unicode.
- wholecell.utils.filepath.run_cmd(tokens, trim=True, timeout=60, env=None, input_=None)[source]
Run a shell command-line (in token list form) and return its stdout. See run_cmd2().
- wholecell.utils.filepath.run_cmd2(tokens, trim=True, timeout=60, env=None, input_=None)[source]
Run a shell command-line (in token list form) and return a tuple containing its (stdout, stderr). This does not expand filename patterns or environment variables or do other shell processing steps.
- Parameters:
tokens (Sequence[str]) – The command line as a list of string tokens.
trim (bool) – Whether to trim off trailing whitespace. This is useful because the outputs usually end with a newline.
timeout (int | None) – timeout in seconds; None for no timeout.
env (dict | None) – optional environment variables for the new process to use instead of inheriting the current process’ environment.
input – input for any prompts that may appear (passed to the subprocess’ stdin)
input_ (str | None) –
- Returns:
The command’s stdout and stderr strings.
- Raises:
OSError (e.g. FileNotFoundError [Python 3] or PermissionError), – subprocess.SubprocessError (TimeoutExpired or CalledProcessError)
- Return type:
- wholecell.utils.filepath.run_cmdline(line, trim=True, timeout=60, input_=None, fallback=None)[source]
Run a shell command-line string then return its output or fallback if it failed. This does not expand filename patterns or environment variables or do other shell processing steps like quoting.
- Parameters:
line (str) – The command line as a string to split.
trim (bool) – Whether to trim off trailing whitespace. This is useful because the subprocess output usually ends with a newline.
timeout (int | None) – timeout in seconds; None for no timeout.
input – input for any prompts that may appear (passed to the subprocess’ stdin)
fallback (str | None) – Return this if the subprocess fails, e.g. trying to run git in a Docker Image that has no git repo.
input_ (str | None) –
- Returns:
The command’s output string, or None if it couldn’t even run.
- Return type:
str | None
- wholecell.utils.filepath.timestamp(dt=None)[source]
Construct a datetime-timestamp from dt [default = now()], such as we use to timestamp a simulation output directory.
- wholecell.utils.filepath.verify_dir_exists(dir_path, message='')[source]
Raise an IOError if dir_path isn’t an existing directory.
- wholecell.utils.filepath.verify_file_exists(file_path, message='')[source]
Raise an IOError if file_path isn’t an existing file.