From 9ed35953c72be4faa929a7f7bebb3c4ea50375a5 Mon Sep 17 00:00:00 2001
From: Jeff Rhoades <37990507+rhoadesScholar@users.noreply.github.com>
Date: Thu, 14 Mar 2024 10:43:11 -0400
Subject: [PATCH 1/4] Update tests.yaml

---
 .github/workflows/tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index 61aa624..8a4319b 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -23,7 +23,7 @@ jobs:
         pip install ".[dev]"
     - name: Test with pytest
       run: |
-        pytest --color=yes --cov={{cookiecutter.project_slug}} --cov-report=xml --cov-report=term-missing tests
+        pytest # --color=yes --cov={{cookiecutter.project_slug}} --cov-report=xml --cov-report=term-missing tests
     # Coverage should work out of the box for public repos. For private repos, more setup is likely required.
     - name: Coverage
       uses: codecov/codecov-action@v4

From a71a1832001d2a81e04cfeb3830e8eb1e3fc5dcf Mon Sep 17 00:00:00 2001
From: Jeff Rhoades <37990507+rhoadesScholar@users.noreply.github.com>
Date: Thu, 14 Mar 2024 10:51:00 -0400
Subject: [PATCH 2/4] Update tests.yaml

---
 .github/workflows/tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index 8a4319b..61aa624 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -23,7 +23,7 @@ jobs:
         pip install ".[dev]"
     - name: Test with pytest
       run: |
-        pytest # --color=yes --cov={{cookiecutter.project_slug}} --cov-report=xml --cov-report=term-missing tests
+        pytest --color=yes --cov={{cookiecutter.project_slug}} --cov-report=xml --cov-report=term-missing tests
     # Coverage should work out of the box for public repos. For private repos, more setup is likely required.
     - name: Coverage
       uses: codecov/codecov-action@v4

From da0495cb044eabac37d5df5f79b09755b5df3bde Mon Sep 17 00:00:00 2001
From: rhoadesScholar <rhoadesj@hhmi.org>
Date: Thu, 14 Mar 2024 10:53:09 -0400
Subject: [PATCH 3/4] =?UTF-8?q?test:=20=E2=9C=85=20Change=20cosem=20model?=
 =?UTF-8?q?=20loading.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Change cosem model loading to replace "." with "_" in model name path, in hopes of passing GitHub Actions tests.
---
 .../__pycache__/__init__.cpython-310.pyc      | Bin 313 -> 313 bytes
 .../__pycache__/utils.cpython-310.pyc         | Bin 1579 -> 1579 bytes
 .../pytorch/cosem/load_model.py               |   6 ++++--
 .../pytorch/cosem/setup26.1/.DS_Store         | Bin 6148 -> 0 bytes
 .../{setup26.1 => setup26_1}/__init__.py      |   0
 .../cosem/{setup26.1 => setup26_1}/model.py   |   0
 6 files changed, 4 insertions(+), 2 deletions(-)
 delete mode 100644 src/cellmap_models/pytorch/cosem/setup26.1/.DS_Store
 rename src/cellmap_models/pytorch/cosem/{setup26.1 => setup26_1}/__init__.py (100%)
 rename src/cellmap_models/pytorch/cosem/{setup26.1 => setup26_1}/model.py (100%)

diff --git a/src/cellmap_models/__pycache__/__init__.cpython-310.pyc b/src/cellmap_models/__pycache__/__init__.cpython-310.pyc
index e649df2c0ccf6054e0a9f07b82b1ca906609b885..073ba4811630152fc9fd9df46c605e117b42ee3b 100644
GIT binary patch
delta 60
zcmdnVw3CTDpO=@50SG3rf1b#_l=0TYjfx8FKz<R3_~ophS5&N@oSKu9n^>S<l#!p9
Ll3JWK@sm3M@wpPy

delta 60
zcmdnVw3CTDpO=@50SNjGUr*#-${00qqoM*EkY5BMemU!h7N-^!>lbC@C#IwpXXyu}
L7UUOC{NxS*;(rob

diff --git a/src/cellmap_models/__pycache__/utils.cpython-310.pyc b/src/cellmap_models/__pycache__/utils.cpython-310.pyc
index ee0ed8d90c502bc4f7a146695a86e272725cde0a..5ec9723fe3183450abc3e80bf39d620cab5594b7 100644
GIT binary patch
delta 190
zcmZ3@vzmuHpO=@50SG3rf8NMFgPHNx<R#1|K=LNDG?4ttYz`!KSzLi+F^i4<EtcH;
zvea8Fd5O8Hnmo6dON(-DF{c!l+~O!G%1<v!EiS&rnU<N88eg1Qm0H9-`5ud<v?kE>
zUk>_tMaBBbsW~~hi3R#a8TpARsl{27jad67wSn@Qj3JurMZ!Q<ksOGS01~$*-(r;#
R1<4kHj6fo^CUdeW0RW@!IC=m8

delta 190
zcmZ3@vzmuHpO=@50SGcOKWyZl!OR#nc?q)#ki5w(4J5xZn*&K*7FQry%wnS-#gdy}
zmU@dNFEKY&lP8L~v?wQvIi<KHild+?KfNfmxcC-lT4qjad~s$~Y7y7udn}gH3P96;
zIp~KLrxq3K7iHuprlb~U=?A42<QGpiV(phy0?KPLhG?=E@dH^!k|06^NJLG(#VREV
Pk}Xm|B@`!fvMB)oC{Qy_

diff --git a/src/cellmap_models/pytorch/cosem/load_model.py b/src/cellmap_models/pytorch/cosem/load_model.py
index 24da416..0f7010b 100755
--- a/src/cellmap_models/pytorch/cosem/load_model.py
+++ b/src/cellmap_models/pytorch/cosem/load_model.py
@@ -46,14 +46,16 @@ def load_model(checkpoint_name: str) -> torch.nn.Module:
     ):
         if checkpoint_name in model_names:
             checkpoint_path = Path(
-                Path(__file__).parent / Path(checkpoint_name) / "model.py"
+                Path(__file__).parent
+                / Path(checkpoint_name.replace(".", "_"))
+                / "model.py"
             )
             no_weights = True
         else:
             raise ValueError(f"Model {checkpoint_name} not found")
     else:
         checkpoint_path = Path(
-            Path(__file__).parent / Path(checkpoint_name)
+            Path(__file__).parent / Path(checkpoint_name.replace(".", "_"))
         ).with_suffix(".pth")
         if not checkpoint_path.exists():
             url = models_dict[checkpoint_name]
diff --git a/src/cellmap_models/pytorch/cosem/setup26.1/.DS_Store b/src/cellmap_models/pytorch/cosem/setup26.1/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3
zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
zLs35+`xjp>T0<F0fCPF1$Cyrb|F7^5{eNG?83~ZUUlGt@xh*qZDeu<Z%US-OSsOPv
j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I

diff --git a/src/cellmap_models/pytorch/cosem/setup26.1/__init__.py b/src/cellmap_models/pytorch/cosem/setup26_1/__init__.py
similarity index 100%
rename from src/cellmap_models/pytorch/cosem/setup26.1/__init__.py
rename to src/cellmap_models/pytorch/cosem/setup26_1/__init__.py
diff --git a/src/cellmap_models/pytorch/cosem/setup26.1/model.py b/src/cellmap_models/pytorch/cosem/setup26_1/model.py
similarity index 100%
rename from src/cellmap_models/pytorch/cosem/setup26.1/model.py
rename to src/cellmap_models/pytorch/cosem/setup26_1/model.py

From b9ed7a844de6edca8f86c4c6d70bdad70c7141f6 Mon Sep 17 00:00:00 2001
From: Jeff Rhoades <37990507+rhoadesScholar@users.noreply.github.com>
Date: Thu, 14 Mar 2024 11:01:45 -0400
Subject: [PATCH 4/4] Update tests.yaml

---
 .github/workflows/tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index 61aa624..cae0eb5 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -23,7 +23,7 @@ jobs:
         pip install ".[dev]"
     - name: Test with pytest
       run: |
-        pytest --color=yes --cov={{cookiecutter.project_slug}} --cov-report=xml --cov-report=term-missing tests
+        pytest --color=yes --cov=cellmap_models --cov-report=xml --cov-report=term-missing tests
     # Coverage should work out of the box for public repos. For private repos, more setup is likely required.
     - name: Coverage
       uses: codecov/codecov-action@v4