misc updates to package boilerplate

Author: reece

.deepsource.toml

@@ -0,0 +1,13 @@
+version = 1
+
+test_patterns = [
+  "tests/**"
+]
+
+[[analyzers]]
+name = "python"
+enabled = true
+runtime_version = "3.x.x"
+
+  [analyzers.meta]
+  max_line_length = 100

.gitignore

@@ -50,6 +50,8 @@
 .scrapy
 .spyderproject
 .spyproject
+.tags
+.tags.mk
 .tox/
 .venv
 .vscode
@@ -61,7 +63,9 @@ __marimo__/
 __pycache__/
 __pypackages__/
 archive
+bdist
 bioutils/_data/assemblies/pull
+build
 build/
 celerybeat-schedule
 celerybeat.pid
@@ -71,7 +75,10 @@ cython_debug/
 develop-eggs/
 dist/
 dmypy.json
+doc*/changelog/*/.tags
+doc*/changelog/*/.tags.mk
 doc/_build
+doc/build
 doc/changelog/*/.tags
 doc/changelog/*/.tags.mk
 doc/changelog/*/hg-git-remap.pl

.mailmap

@@ -1,7 +1,8 @@
+# This file is used by Git to consolidate the users who used multiple accounts
+# I pick the account with the most modified files in git shortlog -sne
 Andreas Prlic <andreas.prlic@invitae.com> Andreas Prlic <36012160+andreas-invitae@users.noreply.github.com>
 Andreas Prlic <andreas.prlic@invitae.com> Andreas Prlic <andreas.prlic@gmail.com>
 Caitlin Gong <ccaitlingo@gmail.com> Caitlin Gong <clgong@vassar.edu>
-# I pick the account with the most modified files in git shortlog -sne
 Katie Stahl <kathryn.stahl@nationwidechildrens.org> katie stahl <kathryn.stahl@nationwidechildrens.org>
 Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de> Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
 Meng <wangm0855@gmail.com> Meng Wang <wangm0855@gmail.com>
@@ -10,4 +11,3 @@ Reece Hart <reecehart@gmail.com> Reece Hart <reece@biocommons.org>
 Reece Hart <reecehart@gmail.com> Reece Hart <reecehart@Reeces-MacBook-Pro.local>
 Reece Hart <reecehart@gmail.com> Reece Hart <reece@ip-192-168-0-13.us-west-2.compute.internal>
 Rudy Rico <rudy.rico@invitae.com> Rudolph Rico <rudy.rico@invitae.com>
-# This is used by Git to consolidate the users who used multiple accounts

tox.ini

@@ -11,7 +11,10 @@ python =
 [testenv]
 allowlist_externals = uv
 commands =
-    uv sync --python {envpython}
-    uv run python -m pytest --doctest-modules tests --cov --cov-config=pyproject.toml --cov-report=xml
-    ty check
+    make test
 passenv = PYTHON_VERSION
+setenv =
+    PYTHONHASHSEED = 0
+usedevelop = True
+whitelist_externals =
+    make