Merge branch 'work'

STOmics · Mar 29, 2024 · 1156e34 · 1156e34
2 parents 28a5109 + 1107d49
commit 1156e34
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diff --git a/.github/workflows/pytest_conda_linux_demo.yml b/.github/workflows/pytest_conda_linux_demo.yml
@@ -11,14 +11,9 @@ on:
 jobs:
   build-linux-and-start-pytest:
     runs-on: cpu
-    defaults:
-      run:
-        shell: bash
     steps:
-    #   - uses: actions/checkout@v3
-      - name: Activate Conda Enviroment
+      - name: 'See Working Dir'
         run: |
-          echo "using conda $(which conda)"
-          conda activate test
+          echo "working dir is $(pwd)"
 
-          echo "using python $(which python)"
+      - uses: actions/checkout@v3
diff --git a/.gitignore b/.gitignore
@@ -136,3 +136,5 @@ tests/test_image/
 tests/test_data/
 
 .vscode/
+
+代码规范.md
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -229,7 +229,7 @@ patchify
 fastremap
 roifile
 cusingler
-cell-bin==1.2.8.1
+cell-bin==1.3.4.1
 
 Sphinx>=7.1.2
 nbsphinx>=0.9.3

diff --git a/docs/source/Tutorials/Cell_Correction.ipynb b/docs/source/Tutorials/Cell_Correction.ipynb
@@ -22,28 +22,6 @@
     "    correcting from GEM and mask."
    ]
   },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "id": "055c2cb0",
-   "metadata": {},
-   "source": [
-    "<div class=\"alert alert-info\">\n",
-    "\n",
-    "**Preparation**\n",
-    "\n",
-    "Before **Cell Segmentation**, **Tissue Segmentation** or generating **mask file** from **ssDNA image** on **Cell Correction**, certain packages should be installed beforehand.  \n",
-    "\n",
-    "Install necessary packages by running commands as below:\n",
-    "\n",
-    "> &ensp;&ensp; **pip install tensorflow==2.7.0**  \n",
-    "> &ensp;&ensp; **pip install torch==1.10.0**  \n",
-    "> &ensp;&ensp; **pip install torchvision==0.11.1**  \n",
-    "> &ensp;&ensp; **pip install albumentations==0.4.6**\n",
-    "\n",
-    "</div>"
-   ]
-  },
   {
    "attachments": {},
    "cell_type": "markdown",

diff --git a/docs/source/Tutorials/Cell_Segmentation.ipynb b/docs/source/Tutorials/Cell_Segmentation.ipynb
diff --git a/docs/source/Tutorials/Clustering_by_GPU.ipynb b/docs/source/Tutorials/Clustering_by_GPU.ipynb
@@ -77,17 +77,9 @@
    "id": "6c54f9b2",
    "metadata": {},
    "source": [
-    "Select the correct version on the homepage of [RAPIDS' official website](https://rapids.ai/start.html). Run following command to build up a specific environment:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6af3dcbf",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "conda create -n rapids-22.12 -c rapidsai -c conda-forge -c nvidia rapids=22.12 python=3.8 cudatoolkit=11.5"
+    "Select the correct version on the homepage of [RAPIDS' official website](https://rapids.ai/start.html). Run following command to build up a specific environment:\n",
+    "\n",
+    "    conda create -y -n stereopy-rapids -c rapidsai -c conda-forge -c nvidia python=3.8 rapids=23.04.01 cuda-version=11.8"
    ]
   },
   {
@@ -120,17 +112,13 @@
    "id": "4d7987c1",
    "metadata": {},
    "source": [
-    "Installation through conda command fails in the environment with GPU acceleration, only [PyPI command](https://stereopy.readthedocs.io/en/latest/General/Installation.html#pypi) will succeed."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ff9da4be",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "pip install stereopy"
+    "Installation through conda command fails in the environment with GPU acceleration, only [PyPI command](https://stereopy.readthedocs.io/en/latest/General/Installation.html#pypi) will succeed.\n",
+    "\n",
+    "    pip install stereopy\n",
+    "\n",
+    "After installing stereopy, you will get some warnings about dependency conflicts, you can ignore them except two that must be reinstall to correct version.\n",
+    "\n",
+    "    pip install dask==2023.3.2 distributed==2023.3.2.1"
    ]
   },
   {

diff --git a/docs/source/Tutorials/SingleR.ipynb b/docs/source/Tutorials/SingleR.ipynb
diff --git a/docs/source/Tutorials/Tissue_Segmentation.ipynb b/docs/source/Tutorials/Tissue_Segmentation.ipynb
diff --git a/docs/source/Tutorials/Trajectory_Analysis.ipynb b/docs/source/Tutorials/Trajectory_Analysis.ipynb