Add jobs to reproduce Cygwin safe.directory submodule issue

Remove the Cygwin xfail decorations from test_submodules in
test_docs.py and test_repo.py, and from test_root_module in
test_submodule.py, so the tests surface the underlying failure
directly. Add 256 reproduce-safe-dir matrix jobs to cygwin-test.yml,
each running these three tests under the current safe.directory
configuration. All or most of these reproduce-safe-dir jobs must be
removed before this work is integrated.

The existing test job's env, defaults, and setup steps gain YAML
anchors so the new job can reference them without duplication.

Root cause hypothesis
---------------------

The CI's safe.directory list (set in the "Special configuration for
Cygwin git" step) covers the main repo and its .git directory but
not the gitdb submodule's working tree at git/ext/gitdb. Git matches
safe.directory exactly, not by prefix, so when GitPython spawns
"git cat-file --batch-check" in the gitdb submodule (via
Repo(submodule_path).odb.info(sha)), git rejects the repository for
dubious ownership and exits.

Three observed failure modes, all from the same root cause
----------------------------------------------------------

The git subprocess exits soon after starting. What Python sees
depends on a race between Python writing to the subprocess's stdin
and the subprocess exiting and closing its stdout pipe.

1. ValueError ("SHA is empty, possible dubious ownership..."):
   Python's write/flush completes before git has finished exiting.
   The buffered write succeeds, then stdout.readline() returns b""
   (EOF). _parse_object_header(b"") in git/cmd.py raises this
   ValueError. The error message names the rejected directory and
   even suggests the safe.directory fix. This propagates uncaught
   from Object.new_from_sha through name_to_object (line 229 of
   git/repo/fun.py is outside the try/except loop) through
   repo.commit("HEAD") to iter_items, where the
   "except (IOError, BadName)" clause does not catch ValueError.

2. IndexError ("list index out of range"):
   Git exits before Python's write/flush runs. cmd.stdin.write or
   cmd.stdin.flush raises BrokenPipeError, a subclass of OSError
   (IOError). This time iter_items's "except (IOError, BadName)"
   catches it, returning an empty iterator. children() therefore
   returns an empty list, and "[0]" in test_submodules raises
   IndexError.

3. AssertionError ("1 not greater than or equal to 2"):
   Same BrokenPipeError-caught-as-IOError mechanism as case 2, but
   manifesting in test_repo.py::test_submodules, which does
   "assertGreaterEqual(len(list(self.rorepo.iter_submodules())), 2)".
   The recursive traversal finds gitdb (via the main repo, which is
   in safe.directory) but cannot enumerate gitdb's children, so
   only one submodule is yielded.

Evidence
--------

Recent main-branch CI runs show all three xfailed tests consistently
matching their raises=ValueError xfail, e.g. job 74546730688 in run
25415738988. Verified across the five most recent main runs.

PR gitpython-developers#2143 attempt 1 (job 74630986491, run 25440735020 attempt 1) had
test_docs.py FAILED with IndexError while test_repo.py XFAILed with
ValueError in the same job. PR gitpython-developers#2143 attempt 2 (job 74633063805) had
both XFAIL with ValueError. Same commit, same workflow, same runner
image -- a flaky race.

The 3-job trial of these reproduce-safe-dir jobs (run 25454533092,
commit baf3526) produced 8 ValueError and 1 IndexError out of 9
test runs.

The 30-job run (run 25454836713) produced 90 ValueError and 0
IndexError in the reproduce jobs, but the same run's test (fast)
job exhibited the AssertionError variant in
test_repo.py::test_submodules. That AssertionError is the third
manifestation of the BrokenPipeError race.

Plan
----

1. (this commit) Reproduce the failure under the current
   safe.directory configuration, with xfails removed so failures
   surface directly. The 256-job matrix is intended to characterize
   the rate of each variant.

2. Apply the fix: extend the safe.directory configuration to cover
   the gitdb submodule's working tree (and smmap's, recursively).
   Verify that the tests now pass.

3. Remove the reproduce-safe-dir jobs and the YAML anchors that
   only the reproduce job needed. The existing test job retains the
   permanent fix.

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: EliahKagan

.github/workflows/cygwin-test.yml

@@ -20,63 +20,73 @@ jobs:
 
     runs-on: windows-latest
 
-    env:
+    env: &cygwin-env
       CHERE_INVOKING: "1"
       CYGWIN_NOWINPATH: "1"
 
-    defaults:
+    defaults: &cygwin-defaults
       run:
         shell: C:\cygwin\bin\bash.exe --login --norc -eo pipefail -o igncr "{0}"
 
     steps:
-    - name: Force LF line endings
+    - &force-lf
+      name: Force LF line endings
       run: |
         git config --global core.autocrlf false  # Affects the non-Cygwin git.
       shell: pwsh  # Do this outside Cygwin, to affect actions/checkout.
 
-    - uses: actions/checkout@v6
+    - &checkout
+      uses: actions/checkout@v6
       with:
         fetch-depth: 0
 
-    - name: Install Cygwin
+    - &install-cygwin
+      name: Install Cygwin
       uses: cygwin/cygwin-install-action@v6
       with:
         packages: git python39 python-pip-wheel python-setuptools-wheel python-wheel-wheel
         add-to-path: false  # No need to change $PATH outside the Cygwin environment.
 
-    - name: Arrange for verbose output
+    - &verbose-output
+      name: Arrange for verbose output
       run: |
         # Arrange for verbose output but without shell environment setup details.
         echo 'set -x' >~/.bash_profile
 
-    - name: Special configuration for Cygwin git
+    - &safe-directory
+      name: Special configuration for Cygwin git
       run: |
         git config --global --add safe.directory "$(pwd)"
         git config --global --add safe.directory "$(pwd)/.git"
         git config --global core.autocrlf false
 
-    - name: Prepare this repo for tests
+    - &prepare-repo
+      name: Prepare this repo for tests
       run: |
         ./init-tests-after-clone.sh
 
-    - name: Set git user identity and command aliases for the tests
+    - &git-identity
+      name: Set git user identity and command aliases for the tests
       run: |
         git config --global user.email "travis@ci.com"
         git config --global user.name "Travis Runner"
         # If we rewrite the user's config by accident, we will mess it up
         # and cause subsequent tests to fail
         cat test/fixtures/.gitconfig >> ~/.gitconfig
 
-    - name: Set up virtual environment
+    - &setup-venv
+      name: Set up virtual environment
       run: |
         python3.9 -m venv .venv
         echo 'BASH_ENV=.venv/bin/activate' >>"$GITHUB_ENV"
 
-    - name: Update PyPA packages
+    - &update-pypa
+      name: Update PyPA packages
       run: |
         python -m pip install -U pip 'setuptools; python_version<"3.12"' wheel
 
-    - name: Install project and test dependencies
+    - &install-deps
+      name: Install project and test dependencies
       run: |
         pip install '.[test]'
 
@@ -91,3 +101,34 @@ jobs:
     - name: Test with pytest (${{ matrix.additional-pytest-args }})
       run: |
         pytest --color=yes -p no:sugar --instafail -vv ${{ matrix.additional-pytest-args }}
+
+  reproduce-safe-dir:
+    strategy:
+      matrix:
+        run: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256]
+      fail-fast: false
+
+    runs-on: windows-latest
+
+    env: *cygwin-env
+
+    defaults: *cygwin-defaults
+
+    steps:
+    - *force-lf
+    - *checkout
+    - *install-cygwin
+    - *verbose-output
+    - *safe-directory
+    - *prepare-repo
+    - *git-identity
+    - *setup-venv
+    - *update-pypa
+    - *install-deps
+
+    - name: Run submodule tests
+      run: |
+        python -m pytest -vv \
+          test/test_docs.py::Tutorials::test_submodules \
+          test/test_repo.py::TestRepo::test_submodules \
+          test/test_submodule.py::TestSubmodule::test_root_module

test/test_docs.py

@@ -6,9 +6,6 @@
 import gc
 import os
 import os.path
-import sys
-
-import pytest
 
 from test.lib import TestBase
 from test.lib.helper import with_rw_directory
@@ -478,11 +475,6 @@ def test_references_and_objects(self, rw_dir):
 
         repo.git.clear_cache()
 
-    @pytest.mark.xfail(
-        sys.platform == "cygwin",
-        reason="Cygwin GitPython can't find SHA for submodule",
-        raises=ValueError,
-    )
     def test_submodules(self):
         # [1-test_submodules]
         repo = self.rorepo

test/test_repo.py

@@ -877,11 +877,6 @@ def test_repo_odbtype(self):
         target_type = GitCmdObjectDB
         self.assertIsInstance(self.rorepo.odb, target_type)
 
-    @pytest.mark.xfail(
-        sys.platform == "cygwin",
-        reason="Cygwin GitPython can't find submodule SHA",
-        raises=ValueError,
-    )
     def test_submodules(self):
         self.assertEqual(len(self.rorepo.submodules), 1)  # non-recursive
         self.assertGreaterEqual(len(list(self.rorepo.iter_submodules())), 2)

test/test_submodule.py

@@ -480,11 +480,6 @@ def test_base_rw(self, rwrepo):
     def test_base_bare(self, rwrepo):
         self._do_base_tests(rwrepo)
 
-    @pytest.mark.xfail(
-        sys.platform == "cygwin",
-        reason="Cygwin GitPython can't find submodule SHA",
-        raises=ValueError,
-    )
     @pytest.mark.xfail(
         HIDE_WINDOWS_KNOWN_ERRORS,
         reason=(