[pre-commit.ci] pre-commit autoupdate (#787)

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.5 → v0.5.7](astral-sh/ruff-pre-commit@v0.5.5...v0.5.7) - [github.com/pre-commit/mirrors-mypy: v1.11.0 → v1.11.1](pre-commit/mirrors-mypy@v1.11.0...v1.11.1) * use types-setuptools instead of types-pkg-resources * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.7 → v0.6.1](astral-sh/ruff-pre-commit@v0.5.7...v0.6.1) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add seed to rng --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eljas Roellin <[email protected]>
theislab · Aug 20, 2024 · fd600ad · fd600ad
1 parent 0ee5c21
commit fd600ad
Show file tree

Hide file tree

Showing 4 changed files with 34 additions and 32 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: prettier
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.5.7
+      rev: v0.6.1
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]

diff --git a/tests/_scripts/catplot_create_expected_plots.ipynb b/tests/_scripts/catplot_create_expected_plots.ipynb
@@ -11,47 +11,46 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
+   "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "import ehrapy as ep"
-   ],
-   "outputs": []
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
+   "outputs": [],
    "source": [
     "%load_ext autoreload\n",
     "%autoreload 2"
-   ],
-   "outputs": []
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 7,
    "metadata": {},
+   "outputs": [],
    "source": [
     "current_notebook_dir = %pwd\n",
     "\n",
     "_TEST_DATA_PATH = f\"{current_notebook_dir}/../test_data/dataset1.csv\"\n",
     "_TEST_IMAGE_PATH = f\"{current_notebook_dir}/../plot/_images\"\n",
-    "adata_mini = ep.io.read_csv(\n",
-    "    _TEST_DATA_PATH, columns_obs_only=[\"glucose\", \"weight\", \"disease\", \"station\"]\n",
-    ")"
-   ],
-   "outputs": []
+    "adata_mini = ep.io.read_csv(_TEST_DATA_PATH, columns_obs_only=[\"glucose\", \"weight\", \"disease\", \"station\"])"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 21,
    "metadata": {},
+   "outputs": [],
    "source": [
     "fig1 = ep.pl.catplot(adata_mini, jitter=False)\n",
     "\n",
     "fig1.savefig(f\"{_TEST_IMAGE_PATH}/catplot_vanilla_expected.png\", dpi=80)"
-   ],
-   "outputs": []
+   ]
   }
  ],
  "metadata": {

diff --git a/tests/_scripts/cohort_tracker_test_create_expected_plots.ipynb b/tests/_scripts/cohort_tracker_test_create_expected_plots.ipynb
@@ -11,46 +11,48 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
+   "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "import ehrapy as ep"
-   ],
-   "outputs": []
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
+   "outputs": [],
    "source": [
     "%load_ext autoreload\n",
     "%autoreload 2"
-   ],
-   "outputs": []
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
+   "outputs": [],
    "source": [
     "current_notebook_dir = %pwd\n",
     "\n",
     "_TEST_DATA_PATH = f\"{current_notebook_dir}/../tools/ehrapy_data/dataset1.csv\"\n",
     "_TEST_IMAGE_PATH = f\"{current_notebook_dir}/../tools/_images\"\n",
     "adata_mini = ep.io.read_csv(_TEST_DATA_PATH, columns_obs_only=[\"glucose\", \"weight\", \"disease\", \"station\"])"
-   ],
-   "outputs": []
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 4,
    "metadata": {},
+   "outputs": [],
    "source": [
     "ct = ep.tl.CohortTracker(adata_mini)\n",
     "\n",
     "ct(adata_mini, label=\"First step\", operations_done=\"Some operations\")\n",
-    "fig1, ax1 = ct.plot_cohort_barplot(show=False, legend_labels={\"weight\": \"weight(kg)\",\"glucose\": \"glucose(mg/dL)\"})\n",
+    "fig1, ax1 = ct.plot_cohort_barplot(show=False, legend_labels={\"weight\": \"weight(kg)\", \"glucose\": \"glucose(mg/dL)\"})\n",
     "ct(adata_mini, label=\"Second step\", operations_done=\"Some other operations\")\n",
-    "fig2, ax2 = ct.plot_cohort_barplot(show=False, legend_labels={\"weight\": \"weight(kg)\",\"glucose\": \"glucose(mg/dL)\"})\n",
+    "fig2, ax2 = ct.plot_cohort_barplot(show=False, legend_labels={\"weight\": \"weight(kg)\", \"glucose\": \"glucose(mg/dL)\"})\n",
     "\n",
     "fig1.savefig(\n",
     "    f\"{_TEST_IMAGE_PATH}/cohorttracker_adata_mini_step1_vanilla_expected.png\",\n",
@@ -61,13 +63,13 @@
     "    f\"{_TEST_IMAGE_PATH}/cohorttracker_adata_mini_step2_vanilla_expected.png\",\n",
     "    dpi=80,\n",
     ")"
-   ],
-   "outputs": []
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
     "ct = ep.tl.CohortTracker(adata_mini)\n",
     "ct(adata_mini, label=\"First step\", operations_done=\"Some operations\")\n",
@@ -81,13 +83,13 @@
     "    f\"{_TEST_IMAGE_PATH}/cohorttracker_adata_mini_step1_use_settings_expected.png\",\n",
     "    dpi=80,\n",
     ")"
-   ],
-   "outputs": []
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
     "ct = ep.tl.CohortTracker(adata_mini)\n",
     "ct(adata_mini, label=\"First step\", operations_done=\"Some operations\")\n",
@@ -103,13 +105,13 @@
     "    f\"{_TEST_IMAGE_PATH}/cohorttracker_adata_mini_step1_use_settings_big_expected.png\",\n",
     "    dpi=80,\n",
     ")"
-   ],
-   "outputs": []
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
     "adata_mini_loose_category = adata_mini.copy()\n",
     "ct = ep.tl.CohortTracker(adata_mini_loose_category)\n",
@@ -118,19 +120,21 @@
     "adata_mini_loose_category = adata_mini_loose_category[adata_mini_loose_category.obs.disease == \"A\", :]\n",
     "ct(adata_mini_loose_category)\n",
     "\n",
-    "fig_loose_category, _ = ct.plot_cohort_barplot(color_palette=\"colorblind\", legend_labels={\"weight\": \"weight(kg)\",\"glucose\": \"glucose(mg/dL)\"}, show=False)\n",
+    "fig_loose_category, _ = ct.plot_cohort_barplot(\n",
+    "    color_palette=\"colorblind\", legend_labels={\"weight\": \"weight(kg)\", \"glucose\": \"glucose(mg/dL)\"}, show=False\n",
+    ")\n",
     "\n",
     "fig_loose_category.savefig(\n",
     "    f\"{_TEST_IMAGE_PATH}/cohorttracker_adata_mini_step2_loose_category_expected.png\",\n",
     "    dpi=80,\n",
     ")"
-   ],
-   "outputs": []
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
     "ct = ep.tl.CohortTracker(adata_mini)\n",
     "\n",
@@ -145,8 +149,7 @@
     "    f\"{_TEST_IMAGE_PATH}/cohorttracker_adata_mini_flowchart_expected.png\",\n",
     "    dpi=80,\n",
     ")"
-   ],
-   "outputs": []
+   ]
   }
  ],
  "metadata": {

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -26,7 +26,7 @@ def root_dir():
 
 @pytest.fixture
 def rng():
-    return np.random.default_rng()
+    return np.random.default_rng(seed=42)
 
 
 @pytest.fixture