change to src layout and pyproject.toml

biocommons · Sep 18, 2023 · d99111a · d99111a
1 parent 60bf045
commit d99111a
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Showing 23 changed files with 89 additions and 118 deletions.
diff --git a/.flake8 b/.flake8
@@ -0,0 +1,6 @@
+# http://pep8.readthedocs.org/en/latest/intro.html#error-codes
+[flake8]
+max-line-length = 120
+exclude = tests/*
+max-complexity = 10
+ignore = E129,E221,E241,E251,E303,W291
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,83 @@
+[project]
+name = "uta"
+dynamic = ["version"]
+description = "Universal Transcript Archive"
+readme = "README.md"
+requires-python = ">=3.5"
+license = {text = "Apache-2.0"}
+
+keywords = [
+    "bioinformatics",
+    "computational biology",
+    "genome variants",
+    "genome variation",
+    "genomic variants",
+    "genomic variation",
+    "genomics",
+    "hgvs",
+]
+
+authors = [
+  {name = "UTA Contributors", email = "[email protected]" }
+]
+maintainers = [
+  {name = "UTA Contributors", email = "[email protected]" }
+]
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python",
+    "Topic :: Database :: Front-Ends",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+
+dependencies = [
+  "attrs",
+  "biocommons.seqrepo",
+  "biopython>=1.69",
+  "bioutils",
+  "colorlog",
+  "configparser",
+  "docopt",
+  "eutils>=0.3.2",
+  "nose",
+  "prettytable",
+  "psycopg2-binary",
+  "pytz",
+  "recordtype",
+  "sqlalchemy",
+  "uta-align",
+]
+
+[project.optional-dependencies]
+test = ["coverage", "testing.postgresql"]
+
+[project.urls]  # Optional
+"Homepage" = "https://github.com/biocommons/uta"
+"Bug Reports" = "https://github.com/biocommons/uta/issues"
+"Source" = "https://github.com/biocommons/uta"
+
+[project.scripts]
+uta = "uta.cli:main"
+
+# This is configuration specific to the `setuptools` build backend.
+# If you are using a different build backend, you will need to change this.
+[tool.setuptools]
+# If there are data files included in your packages that need to be
+# installed, specify them here.
+package-data = {"sample" = ["*.dat"]}
+
+[build-system]
+requires = [
+  "setuptools>=43.0.0",
+  "setuptools_scm==1.11.1",
+  "wheel"
+]
+build-backend = "setuptools.build_meta"
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/uta/__init__.py → src/uta/__init__.py b/uta/__init__.py → src/uta/__init__.py
diff --git a/uta/cli.py → src/uta/cli.py b/uta/cli.py → src/uta/cli.py
diff --git a/uta/etc/logging.conf → src/uta/etc/logging.conf b/uta/etc/logging.conf → src/uta/etc/logging.conf
diff --git a/uta/exceptions.py → src/uta/exceptions.py b/uta/exceptions.py → src/uta/exceptions.py
diff --git a/uta/formats/__init__.py → src/uta/formats/__init__.py b/uta/formats/__init__.py → src/uta/formats/__init__.py
diff --git a/uta/formats/exonset.py → src/uta/formats/exonset.py b/uta/formats/exonset.py → src/uta/formats/exonset.py
diff --git a/uta/formats/geneaccessions.py → src/uta/formats/geneaccessions.py b/uta/formats/geneaccessions.py → src/uta/formats/geneaccessions.py
diff --git a/uta/formats/geneinfo.py → src/uta/formats/geneinfo.py b/uta/formats/geneinfo.py → src/uta/formats/geneinfo.py
diff --git a/uta/formats/ncbitsv.py → src/uta/formats/ncbitsv.py b/uta/formats/ncbitsv.py → src/uta/formats/ncbitsv.py
diff --git a/uta/formats/seqinfo.py → src/uta/formats/seqinfo.py b/uta/formats/seqinfo.py → src/uta/formats/seqinfo.py
diff --git a/uta/formats/txinfo.py → src/uta/formats/txinfo.py b/uta/formats/txinfo.py → src/uta/formats/txinfo.py
diff --git a/uta/loading.py → src/uta/loading.py b/uta/loading.py → src/uta/loading.py
diff --git a/uta/lru_cache.py → src/uta/lru_cache.py b/uta/lru_cache.py → src/uta/lru_cache.py
diff --git a/uta/models.py → src/uta/models.py b/uta/models.py → src/uta/models.py
diff --git a/uta/parsers/__init__.py → src/uta/parsers/__init__.py b/uta/parsers/__init__.py → src/uta/parsers/__init__.py
diff --git a/uta/parsers/geneinfo.py → src/uta/parsers/geneinfo.py b/uta/parsers/geneinfo.py → src/uta/parsers/geneinfo.py
diff --git a/uta/parsers/seqgene.py → src/uta/parsers/seqgene.py b/uta/parsers/seqgene.py → src/uta/parsers/seqgene.py
diff --git a/uta/tools/__init__.py → src/uta/tools/__init__.py b/uta/tools/__init__.py → src/uta/tools/__init__.py
diff --git a/tests/__init__.py b/tests/__init__.py