cool-seq-tool 0.4.0.dev0__tar.gz → 0.4.0.dev2__tar.gz

{cool_seq_tool-0.4.0.dev0/src/cool_seq_tool.egg-info → cool_seq_tool-0.4.0.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.4.0.dev0
+Version: 0.4.0.dev2
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -49,7 +49,7 @@ License-File: LICENSE
 Requires-Dist: asyncpg
 Requires-Dist: aiofiles
 Requires-Dist: boto3
-Requires-Dist: pyliftover
+Requires-Dist: agct>=0.1.0-dev1
 Requires-Dist: polars
 Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
@@ -62,7 +62,7 @@ Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
+Requires-Dist: ruff>=0.1.14; extra == "dev"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -75,12 +75,13 @@ Requires-Dist: sphinx-autobuild==2021.3.14; extra == "docs"
 Requires-Dist: sphinx-copybutton==0.5.2; extra == "docs"
 Requires-Dist: sphinxext-opengraph==0.8.2; extra == "docs"
 Requires-Dist: furo==2023.3.27; extra == "docs"
+Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
 
 <h1 align="center">
 CoolSeqTool
 </h1>
 
-**[Documentation](https://coolseqtool.readthedocs.io/en/latest/)** · [Installation](https://coolseqtool.readthedocs.io/en/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/en/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/en/latest/reference/index.html)
+**[Documentation](https://coolseqtool.readthedocs.io/latest/)** · [Installation](https://coolseqtool.readthedocs.io/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/latest/reference/index.html)
 
 ## Overview
 
@@ -102,7 +103,7 @@ CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
 python3 -m pip install cool-seq-tool
 ```
 
-See the [installation instructions](https://coolseqtool.readthedocs.io/en/latest/install.html) in the documentation for a description of dependency setup requirements.
+See the [installation instructions](https://coolseqtool.readthedocs.io/latest/install.html) in the documentation for a description of dependency setup requirements.
 
 ---
 
@@ -127,4 +128,4 @@ All CoolSeqTool resources can be initialized by way of a top-level class instanc
 
 ## Feedback and contributing
 
-We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/en/latest/contributing.html) contains guidance for submitting feedback and contributing new code.
+We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/latest/contributing.html) contains guidance for submitting feedback and contributing new code.

{cool_seq_tool-0.4.0.dev0 → cool_seq_tool-0.4.0.dev2}/README.md

@@ -2,7 +2,7 @@
 CoolSeqTool
 </h1>
 
-**[Documentation](https://coolseqtool.readthedocs.io/en/latest/)** · [Installation](https://coolseqtool.readthedocs.io/en/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/en/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/en/latest/reference/index.html)
+**[Documentation](https://coolseqtool.readthedocs.io/latest/)** · [Installation](https://coolseqtool.readthedocs.io/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/latest/reference/index.html)
 
 ## Overview
 
@@ -24,7 +24,7 @@ CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
 python3 -m pip install cool-seq-tool
 ```
 
-See the [installation instructions](https://coolseqtool.readthedocs.io/en/latest/install.html) in the documentation for a description of dependency setup requirements.
+See the [installation instructions](https://coolseqtool.readthedocs.io/latest/install.html) in the documentation for a description of dependency setup requirements.
 
 ---
 
@@ -49,4 +49,4 @@ All CoolSeqTool resources can be initialized by way of a top-level class instanc
 
 ## Feedback and contributing
 
-We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/en/latest/contributing.html) contains guidance for submitting feedback and contributing new code.
+We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/latest/contributing.html) contains guidance for submitting feedback and contributing new code.

{cool_seq_tool-0.4.0.dev0 → cool_seq_tool-0.4.0.dev2}/pyproject.toml

@@ -29,7 +29,7 @@ dependencies = [
     "asyncpg",
     "aiofiles",
     "boto3",
-    "pyliftover",
+    "agct >= 0.1.0-dev1",
     "polars",
     "hgvs",
     "biocommons.seqrepo",
@@ -41,7 +41,7 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-dev = ["pre-commit", "ipython", "ipykernel", "psycopg2-binary", "ruff"]
+dev = ["pre-commit", "ipython", "ipykernel", "psycopg2-binary", "ruff>=0.1.14"]
 tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
 docs = [
     "sphinx==6.1.3",
@@ -50,6 +50,7 @@ docs = [
     "sphinx-copybutton==0.5.2",
     "sphinxext-opengraph==0.8.2",
     "furo==2023.3.27",
+    "sphinx-github-changelog==1.2.1"
 ]
 
 [project.urls]
@@ -66,8 +67,15 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools.dynamic]
 version = {attr = "cool_seq_tool.version.__version__"}
 
-[tool.setuptools.packages.find]
-where = ["src"]
+# Scanning for namespace packages in the ``src`` directory is true by
+# default in pyproject.toml, so you do NOT need to include the
+# `tool.setuptools.packages.find` if it looks like the following:
+# [tool.setuptools.packages.find]
+# namespaces = true
+# where = ["src"]
+
+[tool.setuptools.package-data]
+"cool_seq_tool.data" = ["transcript_mapping.tsv"]
 
 [tool.pytest.ini_options]
 addopts = "--cov=src --cov-report term-missing"
@@ -79,14 +87,49 @@ branch = true
 [tool.ruff]
 src = ["src"]
 exclude = ["docs/source/conf.py"]
-# pycodestyle (E, W)
-# Pyflakes (F)
-# flake8-annotations (ANN)
-# pydocstyle (D)
-# pep8-naming (N)
-# isort (I)
-select = ["E", "W", "F", "ANN", "D", "N", "I"]
-fixable = ["I", "F401"]
+select = [
+    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
+    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
+    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+    "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+    "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+    "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
+    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+    "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+    "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+    "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
+    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+    "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+]
+fixable = [
+    "I",
+    "F401",
+    "D",
+    "UP",
+    "ANN",
+    "B",
+    "C4",
+    "G",
+    "PIE",
+    "PT",
+    "RSE",
+    "SIM",
+    "RUF"
+]
 
 # ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
@@ -102,12 +145,14 @@ fixable = ["I", "F401"]
 # E117 - over-indented*
 # E501 - line-too-long*
 # W191 - tab-indentation*
+# S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
 ignore = [
     "ANN101", "ANN003",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
-    "W191"
+    "W191",
+    "S321",
 ]
 
 [tool.ruff.per-file-ignores]
@@ -117,6 +162,9 @@ ignore = [
 # N805 - invalid-first-argument-name-for-method
 # F821 - undefined-name
 # F401 - unused-import
-"tests/*" = ["ANN001", "ANN2", "ANN102"]
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101"]
 "*__init__.py" = ["F401"]
 "src/cool_seq_tool/schemas.py" = ["ANN201", "N805", "ANN001"]
+
+[tool.ruff.lint.flake8-bugbear]
+extend-immutable-calls = ["fastapi.Query"]

cool_seq_tool-0.4.0.dev2/src/cool_seq_tool/data/__init__.py

@@ -0,0 +1,2 @@
+"""Module for data"""
+from .data_downloads import DataDownload

{cool_seq_tool-0.4.0.dev0 → cool_seq_tool-0.4.0.dev2}/src/cool_seq_tool/data/data_downloads.py

@@ -4,7 +4,6 @@ import gzip
 import logging
 import shutil
 from ftplib import FTP
-from os import remove
 from pathlib import Path
 
 from dateutil import parser
@@ -38,18 +37,20 @@ class DataDownload:
             files = ftp.nlst()
             mane_summary_file = [f for f in files if f.endswith(".summary.txt.gz")]
             if not mane_summary_file:
-                raise Exception("Unable to download MANE summary data")
+                msg = "Unable to download MANE summary data"
+                raise Exception(msg)
             mane_summary_file = mane_summary_file[0]
             self._mane_summary_path = self._data_dir / mane_summary_file[:-3]
             mane_data_path = self._data_dir / mane_summary_file
             if not self._mane_summary_path.exists():
                 logger.info("Downloading MANE summary file from NCBI.")
-                with open(mane_data_path, "wb") as fp:
+                with mane_data_path.open("wb") as fp:
                     ftp.retrbinary(f"RETR {mane_summary_file}", fp.write)
-                with gzip.open(mane_data_path, "rb") as f_in:
-                    with open(self._mane_summary_path, "wb") as f_out:
-                        shutil.copyfileobj(f_in, f_out)
-                remove(mane_data_path)
+                with gzip.open(
+                    mane_data_path, "rb"
+                ) as f_in, self._mane_summary_path.open("wb") as f_out:
+                    shutil.copyfileobj(f_in, f_out)
+                mane_data_path.unlink()
                 logger.info("MANE summary file download complete.")
         return self._mane_summary_path
 
@@ -66,18 +67,23 @@ class DataDownload:
             ftp_file_path = f"{ftp_dir_path}{lrg_refseqgene_file}"
             timestamp = ftp.voidcmd(f"MDTM {ftp_file_path}")[4:].strip()
             date = str(parser.parse(timestamp)).split()[0]
-            version = datetime.datetime.strptime(date, "%Y-%m-%d").strftime("%Y%m%d")
+            version = (
+                datetime.datetime.strptime(date, "%Y-%m-%d")
+                .astimezone(tz=datetime.timezone.utc)
+                .strftime("%Y%m%d")
+            )
             fn_versioned = f"{lrg_refseqgene_file}_{version}"
             lrg_refseqgene_path = self._data_dir / lrg_refseqgene_file
             self._lrg_refseqgene_path = self._data_dir / fn_versioned
             if not self._lrg_refseqgene_path.exists():
                 logger.info("Downloading LRG RefSeq data from NCBI.")
                 ftp.cwd(ftp_dir_path)
-                with open(lrg_refseqgene_path, "wb") as fp:
+                with lrg_refseqgene_path.open("wb") as fp:
                     ftp.retrbinary(f"RETR {lrg_refseqgene_file}", fp.write)
-                with open(lrg_refseqgene_path, "rb") as f_in:
-                    with open(self._lrg_refseqgene_path, "wb") as f_out:
-                        shutil.copyfileobj(f_in, f_out)
-                remove(lrg_refseqgene_path)
+                with lrg_refseqgene_path.open(
+                    "rb"
+                ) as f_in, self._lrg_refseqgene_path.open("wb") as f_out:
+                    shutil.copyfileobj(f_in, f_out)
+                lrg_refseqgene_path.unlink()
                 logger.info("LRG RefSeq data download complete.")
         return self._lrg_refseqgene_path