update to pytometry 0.1.5

saeyslab · Aug 8, 2024 · 5a1efd9 · 5a1efd9
1 parent b7ae45a
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diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb
@@ -25,7 +25,7 @@
     "## Loading in the data\n",
     "\n",
     "FlowSOM handles different inputs, such as an anndata object by pytometry or a filepath. For this purpose we will make use of an anndata object. This allows\n",
-    "easier preprocessing. Note that this requires also installing the [pytometry](https://github.com/scverse/pytometry) package (version > 0.1.5) with e.g. `pip install git+https://github.com/scverse/pytometry.git@main`.\n"
+    "easier preprocessing. Note that this requires also installing the [pytometry](https://github.com/scverse/pytometry) package (version > 0.1.5) with e.g. `pip install pytometry`.\n"
    ]
   },
   {
@@ -521,9 +521,9 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\u001b[32m2024-07-05 13:59:37.117\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m84\u001b[0m - \u001b[34m\u001b[1mReading input.\u001b[0m\n",
-      "\u001b[32m2024-07-05 13:59:37.119\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m86\u001b[0m - \u001b[34m\u001b[1mFitting model: clustering and metaclustering.\u001b[0m\n",
-      "\u001b[32m2024-07-05 13:59:38.365\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m88\u001b[0m - \u001b[34m\u001b[1mUpdating derived values.\u001b[0m\n"
+      "\u001b[32m2024-08-08 16:44:21.060\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m84\u001b[0m - \u001b[34m\u001b[1mReading input.\u001b[0m\n",
+      "\u001b[32m2024-08-08 16:44:21.064\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m86\u001b[0m - \u001b[34m\u001b[1mFitting model: clustering and metaclustering.\u001b[0m\n",
+      "\u001b[32m2024-08-08 16:44:23.154\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m88\u001b[0m - \u001b[34m\u001b[1mUpdating derived values.\u001b[0m\n"
      ]
     }
    ],
@@ -1582,9 +1582,9 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\u001b[32m2024-07-05 13:59:38.759\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m84\u001b[0m - \u001b[34m\u001b[1mReading input.\u001b[0m\n",
-      "\u001b[32m2024-07-05 13:59:38.761\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m86\u001b[0m - \u001b[34m\u001b[1mFitting model: clustering and metaclustering.\u001b[0m\n",
-      "\u001b[32m2024-07-05 13:59:38.945\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m88\u001b[0m - \u001b[34m\u001b[1mUpdating derived values.\u001b[0m\n"
+      "\u001b[32m2024-08-08 16:44:23.665\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m84\u001b[0m - \u001b[34m\u001b[1mReading input.\u001b[0m\n",
+      "\u001b[32m2024-08-08 16:44:23.667\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m86\u001b[0m - \u001b[34m\u001b[1mFitting model: clustering and metaclustering.\u001b[0m\n",
+      "\u001b[32m2024-08-08 16:44:23.870\u001b[0m | \u001b[34m\u001b[1mDEBUG   \u001b[0m | \u001b[36mflowsom.main\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m88\u001b[0m - \u001b[34m\u001b[1mUpdating derived values.\u001b[0m\n"
      ]
     },
     {
@@ -2171,9 +2171,9 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/benjaminr/Documents/GitHub/FlowSOM/src/flowsom/pp/fcs_functions.py:48: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.\n",
+      "/Users/benjaminr/Documents/GitHub/FlowSOM/src/flowsom/pp/fcs_functions.py:47: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.\n",
       "  f.obs[\"Original_ID\"] = np.array(ids, dtype=np.float32)\n",
-      "/Users/benjaminr/Documents/GitHub/FlowSOM/src/flowsom/pp/fcs_functions.py:48: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.\n",
+      "/Users/benjaminr/Documents/GitHub/FlowSOM/src/flowsom/pp/fcs_functions.py:47: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.\n",
       "  f.obs[\"Original_ID\"] = np.array(ids, dtype=np.float32)\n",
       "/opt/homebrew/Caskroom/mambaforge/base/envs/flowsom/lib/python3.12/site-packages/anndata/_core/anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n",
       "  utils.warn_names_duplicates(\"obs\")\n"

diff --git a/pyproject.toml b/pyproject.toml
@@ -57,8 +57,7 @@ doc = [
     "ipython",
     "sphinx-copybutton",
     # For example notebooks
-    # TODO: pin to >0.1.5
-    "pytometry",
+    "pytometry>=0.1.5",
 ]
 test = ["pytest", "coverage"]