From 599ce4e65be43bc0991d2804dd27fdd4f8cc0cfd Mon Sep 17 00:00:00 2001
From: Jakub Kaczmarzyk <jakub.kaczmarzyk@gmail.com>
Date: Mon, 9 Jan 2023 13:01:15 -0500
Subject: [PATCH 1/3] add geojson to dev + test that converted geojson is valid

---
 setup.cfg         | 1 +
 tests/test_all.py | 4 +++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 1bf0836..bcde65f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -49,6 +49,7 @@ install_requires =
 dev =
     black
     flake8
+    geojson
     imagecodecs  # for tifffile
     mypy
     pytest
diff --git a/tests/test_all.py b/tests/test_all.py
index a6d26fd..4f276e9 100644
--- a/tests/test_all.py
+++ b/tests/test_all.py
@@ -7,6 +7,7 @@
 from typing import List
 
 from click.testing import CliRunner
+import geojson as geojsoblib
 import h5py
 import numpy as np
 import pandas as pd
@@ -323,7 +324,8 @@ def test_cli_run_regression(
     result = runner.invoke(cli, ["togeojson", str(results_dir), str(geojson_dir)])
     assert result.exit_code == 0
     with open(geojson_dir / "purple.json") as f:
-        d = json.load(f)
+        d: geojsoblib.GeoJSON = geojsoblib.load(f)
+    assert d.is_valid, "geojson not valid!"
     assert len(d["features"]) == expected_num_patches
 
     for geojson_row in d["features"]:

From 78d59f1b5409ca0fe1d6bfc1f8ecf2fa0af3b627 Mon Sep 17 00:00:00 2001
From: Jakub Kaczmarzyk <jakub.kaczmarzyk@gmail.com>
Date: Mon, 9 Jan 2023 13:10:20 -0500
Subject: [PATCH 2/3] update copyright year to 2023

---
 docs/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/conf.py b/docs/conf.py
index 0da0bef..cfe2276 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -7,7 +7,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = "wsinfer"
-copyright = "2022, Jakub Kaczmarzyk"
+copyright = "2023, Jakub Kaczmarzyk"
 author = "Jakub Kaczmarzyk"
 
 # -- General configuration ---------------------------------------------------

From 45feee1443c33761dee663c7a98a8476ae2d0463 Mon Sep 17 00:00:00 2001
From: Jakub Kaczmarzyk <jakub.kaczmarzyk@gmail.com>
Date: Mon, 9 Jan 2023 13:15:19 -0500
Subject: [PATCH 3/3] fix type errors

---
 tests/test_all.py | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/tests/test_all.py b/tests/test_all.py
index 4f276e9..ef5637f 100644
--- a/tests/test_all.py
+++ b/tests/test_all.py
@@ -98,13 +98,13 @@ def test_cli_list(tmp_path: Path):
     )
     assert ret.returncode == 0
     output = ret.stdout.decode()
-    assert configs[0]["name"] in output
-    assert configs[0]["architecture"] in output
-    assert configs[1]["name"] in output
-    assert configs[1]["architecture"] in output
+    assert configs[0]["name"] in output  # type: ignore
+    assert configs[0]["architecture"] in output  # type: ignore
+    assert configs[1]["name"] in output  # type: ignore
+    assert configs[1]["architecture"] in output  # type: ignore
     # Negative control.
     ret = subprocess.run([sys.executable, "-m", "wsinfer", "list"], capture_output=True)
-    assert configs[0]["name"] not in ret.stdout.decode()
+    assert configs[0]["name"] not in ret.stdout.decode()  # type: ignore
     del config_root_single, output, ret, config
 
     # Test of WSINFER_PATH registration... check that the models appear in list.
@@ -124,12 +124,12 @@ def test_cli_list(tmp_path: Path):
     )
     assert ret.returncode == 0
     output = ret.stdout.decode()
-    assert configs[0]["name"] in output
-    assert configs[0]["architecture"] in output
-    assert configs[1]["name"] in output
-    assert configs[1]["architecture"] in output
+    assert configs[0]["name"] in output  # type: ignore
+    assert configs[0]["architecture"] in output  # type: ignore
+    assert configs[1]["name"] in output  # type: ignore
+    assert configs[1]["architecture"] in output  # type: ignore
     ret = subprocess.run([sys.executable, "-m", "wsinfer", "list"], capture_output=True)
-    assert configs[0]["name"] not in ret.stdout.decode()
+    assert configs[0]["name"] not in ret.stdout.decode()  # type: ignore
 
 
 def test_cli_run_args(tmp_path: Path):
@@ -143,9 +143,9 @@ def test_cli_run_args(tmp_path: Path):
     args = [
         "run",
         "--wsi-dir",
-        wsi_dir,
+        str(wsi_dir),
         "--results-dir",
-        tmp_path / "results",
+        str(tmp_path / "results"),
     ]
     # No model, weights, or config.
     result = runner.invoke(cli, args)
@@ -257,7 +257,7 @@ def test_cli_run_args(tmp_path: Path):
 def test_cli_run_regression(
     model: str,
     weights: str,
-    class_names: List[float],
+    class_names: List[str],
     expected_probs: List[float],
     expected_patch_size: int,
     expected_num_patches: int,
@@ -274,13 +274,13 @@ def test_cli_run_regression(
         [
             "run",
             "--wsi-dir",
-            tiff_image.parent,
+            str(tiff_image.parent),
             "--model",
             model,
             "--weights",
             weights,
             "--results-dir",
-            results_dir,
+            str(results_dir),
         ],
     )
     assert result.exit_code == 0
@@ -381,11 +381,11 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         [
             "run",
             "--wsi-dir",
-            tiff_image.parent,
+            str(tiff_image.parent),
             "--config",
-            config,
+            str(config),
             "--results-dir",
-            results_dir,
+            str(results_dir),
         ],
     )
     assert result.exit_code == 0