chore: pipelines are passing.

README.md

-# BiTIA CLI
+# BioInformatics Tool for Infrastructure Automation (BiTIA) CLI utility
+
+This is the cli utility of the BiTIA project. The other component is
+`bitia-runner`. Most users only need the cli client `bitia` to submit jobs.
+Install it using pip.
+
+```
+pip install bitia
+```
+
+## BiTIA runner
+
+If you are self-hosting the BiTIA server, you need `bitia-runner` as well. See
+the documents of `bitia-runner` for more details.

bitia/__init__.py

+from importlib.metadata import version as _version
+import os
+import logging
+from rich.logging import RichHandler
+import logging.handlers
+
+log_level = os.environ.get("BITIA_LOGLEVEL", "NOTSET").upper()
+logging.basicConfig(
+    format="%(message)s",
+    level=log_level,
+    datefmt="[%X]",
+    handlers=[RichHandler(rich_tracebacks=True)],
+)
+
+__version__ = _version("bitia")
+
+
+def version() -> str:
+    """version"""
+    return __version__

bitia/__main__.py

@@ -14,7 +14,8 @@ from rich.logging import RichHandler
 
 from pathlib import Path
 import tempfile
-from checksumdir import dirhash
+
+from bitia.checksumdir import dirhash
 
 FORMAT = "%(message)s"
 logging.basicConfig(

bitia/checksumdir.py

+"""
+Function for deterministically creating a single hash for a directory of files,
+taking into account only file contents and not filenames.
+
+dirhash('/path/to/directory', 'md5')
+
+Orignally from
+https://raw.githubusercontent.com/SubconsciousCompute/checksumdir/master/checksumdir/__init__.p
+y
+
+"""
+
+import hashlib
+import typing as T
+import os
+import re
+from pathlib import Path
+
+HASH_FUNCS = {
+    "md5": hashlib.md5,
+    "sha1": hashlib.sha1,
+    "sha256": hashlib.sha256,
+    "sha512": hashlib.sha512,
+}
+
+
+def dirhash(
+    dirname: Path,
+    hashfunc: str = "md5",
+    excluded_files: T.List[Path] = [],
+    ignore_hidden: bool = False,
+    followlinks: bool = False,
+    excluded_extensions: T.List[str] = [],
+):
+    hash_func = HASH_FUNCS[hashfunc]
+    assert dirname.is_dir(), "{} is not a directory.".format(dirname)
+    hashvalues = []
+    for r_dir, dirs, files in os.walk(dirname, topdown=True, followlinks=followlinks):
+        if ignore_hidden and re.search(r"/\.", r_dir):
+            continue
+        root = Path(r_dir)
+        dirs.sort()
+        files.sort()
+        for fname in files:
+            if ignore_hidden and fname.startswith("."):
+                continue
+
+            if Path(fname).suffix in excluded_extensions:
+                continue
+
+            if fname in excluded_files:
+                continue
+
+            hashvalues.append(filehash(root / fname, hashfunc))
+
+    return _reduce_hash(hashvalues, hash_func)
+
+
+def filehash(filepath: Path, hashfunc: str = "md5"):
+    hasher = HASH_FUNCS[hashfunc]()
+    blocksize = 64 * 1024
+
+    if not filepath.is_file():
+        return hasher.hexdigest()
+
+    with filepath.open("rb") as fp:
+        while True:
+            data = fp.read(blocksize)
+            if not data:
+                break
+            hasher.update(data)
+    return hasher.hexdigest()
+
+
+def _reduce_hash(hashlist, hashfunc):
+    hasher = hashfunc()
+    for hashvalue in sorted(hashlist):
+        hasher.update(hashvalue.encode("utf-8"))
+    return hasher.hexdigest()

poetry.lock

@@ -17,14 +17,6 @@ python-versions = ">=3.6.0"
 [package.extras]
 unicode_backport = ["unicodedata2"]
 
-[[package]]
-name = "checksumdir"
-version = "1.2.0"
-description = "Compute a single hash of the file contents of a directory."
-category = "main"
-optional = false
-python-versions = ">=3.6,<4.0"
-
 [[package]]
 name = "click"
 version = "8.1.3"
@@ -149,7 +141,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.8"
-content-hash = "d60f75638b8835d054e6d589945791f581eb9275aae90e255a58aff3bfab3b27"
+content-hash = "876b8c11170f017ce20e5b481e80612ab81476f22aa411f669ad5edcc0fdd327"
 
 [metadata.files]
 certifi = [
@@ -160,10 +152,6 @@ charset-normalizer = [
     {file = "charset-normalizer-2.1.1.tar.gz", hash = "sha256:5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845"},
     {file = "charset_normalizer-2.1.1-py3-none-any.whl", hash = "sha256:83e9a75d1911279afd89352c68b45348559d1fc0506b054b346651b5e7fee29f"},
 ]
-checksumdir = [
-    {file = "checksumdir-1.2.0-py3-none-any.whl", hash = "sha256:77687e16da95970c94061c74ef2e13666c4b6e0e8c90a5eaf0c8f7591332cf01"},
-    {file = "checksumdir-1.2.0.tar.gz", hash = "sha256:10bfd7518da5a14b0e9ac03e9ad105f0e70f58bba52b6e9aa2f21a3f73c7b5a8"},
-]
 click = [
     {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
     {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},

pyproject.toml

 [tool.poetry]
 name = "bitia"
 version = "0.1.1"
-description = "BioInformatics Tool for Infrastructure Automation (BiTIA) command line utility."
+description = "BioInformatics Tool for Infrastructure Automation (BiTIA) CLI utility."
 authors = ["Dilawar Singh <dilawar@subcom.tech>"]
 readme = "README.md"
 
@@ -9,7 +9,6 @@ readme = "README.md"
 python = "^3.8"
 requests = "^2.28.1"
 typer = "^0.6.1"
-checksumdir = "^1.2.0"
 rich = "^12.5.1"
 
 [tool.poetry.scripts]

tests/test_sanity.py

+import bitia
+
+
+def test_sanity():
+    assert bitia.version()