Merge branch 'main' into efficient

.github/workflows/docker-image.yml

@@ -11,6 +11,6 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
             - name: Build the Docker image
               run: docker build . --file Dockerfile --tag ${{ github.repository }}:$(date +%s)

.github/workflows/docker-publish.yml

@@ -13,7 +13,7 @@ jobs:
             contents: read
         steps:
             - name: Check out the repo
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
 
             - name: Log in to Docker Hub
               uses: docker/login-action@v2

.github/workflows/docs-build.yml

@@ -7,12 +7,12 @@ jobs:
     deploy:
         runs-on: ubuntu-latest
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
               with:
                   fetch-depth: 0
-            - uses: actions/setup-python@v4
+            - uses: actions/setup-python@v5
               with:
-                  python-version: "3.10"
+                  python-version: "3.11"
             - name: Install GDAL
               run: |
                   python -m pip install --upgrade pip
@@ -26,11 +26,6 @@ jobs:
                   pip install --no-cache-dir Cython
                   pip install -r requirements.txt -r requirements_dev.txt -r requirements_docs.txt
                   pip install .
-            - name: Discover typos with codespell
-              run: codespell --skip="*.csv,*.geojson,*.json,*.js,*.html,*cff,*.pdf" --ignore-words-list="aci,acount,acounts,fallow,hart,hist,nd,ned,ois,wqs,pres"
-            # - name: PKG-TEST
-            #   run: |
-            #       python -m unittest discover tests/
             - run: mkdocs build
             - name: Deploy to Netlify
               uses: nwtgck/actions-netlify@v2.0

.github/workflows/docs.yml

@@ -7,10 +7,10 @@ jobs:
     deploy:
         runs-on: ubuntu-latest
         steps:
-            - uses: actions/checkout@v3
-            - uses: actions/setup-python@v4
+            - uses: actions/checkout@v4
+            - uses: actions/setup-python@v5
               with:
-                  python-version: 3.9
+                  python-version: "3.11"
             - name: Install dependencies
               run: |
                   python -m pip install --upgrade pip

.github/workflows/draft-pdf.yml

@@ -6,7 +6,7 @@ jobs:
         name: Paper Draft
         steps:
             - name: Checkout
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
             - name: Build draft PDF
               uses: openjournals/openjournals-draft-action@master
               with:

.github/workflows/macos.yml

@@ -15,14 +15,14 @@ jobs:
             fail-fast: false
             matrix:
                 config:
-                    - { os: macOS-latest, py: "3.10" }
+                    - { os: macOS-latest, py: "3.11" }
         env:
             SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
         steps:
             - name: CHECKOUT CODE
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
             - name: SETUP PYTHON
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.config.py }}
             # - name: Install GDAL

.github/workflows/pypi.yml

@@ -12,9 +12,9 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
             - name: Set up Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: "3.x"
             - name: Install dependencies

.github/workflows/ubuntu.yml

@@ -24,9 +24,9 @@ jobs:
             SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
         steps:
             - name: CHECKOUT CODE
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
             - name: SETUP PYTHON
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.config.py }}
             - name: Install GDAL

.github/workflows/windows.yml

@@ -11,9 +11,9 @@ jobs:
     test-windows:
         runs-on: windows-latest
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
             - name: Install miniconda
-              uses: conda-incubator/setup-miniconda@v2
+              uses: conda-incubator/setup-miniconda@v3
               with:
                   auto-activate-base: true
                   python-version: "3.10"

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.6.0
+      hooks:
+          - id: check-toml
+          - id: check-yaml
+          - id: end-of-file-fixer
+            types: [python]
+          - id: trailing-whitespace
+          - id: requirements-txt-fixer
+          - id: check-added-large-files
+            args: ["--maxkb=500"]
+
+    - repo: https://github.com/psf/black
+      rev: 24.4.2
+      hooks:
+          - id: black-jupyter
+            language_version: python3.11
+
+    - repo: https://github.com/codespell-project/codespell
+      rev: v2.2.6
+      hooks:
+          - id: codespell
+            args: [--toml, pyproject-codespell.precommit-toml]
+
+    - repo: https://github.com/kynan/nbstripout
+      rev: 0.7.1
+      hooks:
+          - id: nbstripout

Dockerfile

@@ -4,7 +4,7 @@ LABEL repo="https://github.com/opengeos/segment-geospatial"
 
 RUN mamba install -c conda-forge leafmap localtileserver segment-geospatial -y && \
     pip install -U segment-geospatial jupyter-server-proxy && \
-    jupyter serverextension enable --sys-prefix jupyter_server_proxy && \
+    jupyter server extension enable --sys-prefix jupyter_server_proxy && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
@@ -18,6 +18,5 @@ ARG LOCALTILESERVER_CLIENT_PREFIX='proxy/{port}'
 ENV LOCALTILESERVER_CLIENT_PREFIX=$LOCALTILESERVER_CLIENT_PREFIX
 
 USER root
-RUN apt update; apt install -y libgl1
 RUN chown -R ${NB_UID} ${HOME}
 USER ${NB_USER}

README.md

@@ -21,7 +21,8 @@ The **segment-geospatial** package draws its inspiration from [segment-anything-
 
 ## Citations
 
--   Wu, Q., & Osco, L. (2023). samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM). _Journal of Open Source Software_, 8(89), 5663, <https://doi.org/10.21105/joss.05663>
+-   Wu, Q., & Osco, L. (2023). samgeo: A Python package for segmenting geospatial data with the Segment Anything Model (SAM). _Journal of Open Source Software_, 8(89), 5663. <https://doi.org/10.21105/joss.05663>
+-   Osco, L. P., Wu, Q., de Lemos, E. L., Gonçalves, W. N., Ramos, A. P. M., Li, J., & Junior, J. M. (2023). The Segment Anything Model (SAM) for remote sensing applications: From zero to one shot. _International Journal of Applied Earth Observation and Geoinformation_, 124, 103540. <https://doi.org/10.1016/j.jag.2023.103540>
 
 ## Features
 
@@ -56,16 +57,16 @@ conda install -c conda-forge mamba
 mamba install -c conda-forge segment-geospatial
 ```
 
-Samgeo-geospatial has some optional dependencies that are not included in the default conda environment. To install these dependencies, run the following command:
+If your system has a GPU, but the above commands do not install the GPU version of pytorch, you can force the installation of the GPU version of pytorch using the following command:
 
 ```bash
-mamba install -c conda-forge groundingdino-py segment-anything-fast
+mamba install -c conda-forge segment-geospatial "pytorch=*=cuda*"
 ```
 
-As of July 9th, 2023 Linux systems have also required that `libgl1` be installed for segment-geospatial to work. The following command will install that dependency
+Samgeo-geospatial has some optional dependencies that are not included in the default conda environment. To install these dependencies, run the following command:
 
 ```bash
-apt update; apt install -y libgl1
+mamba install -c conda-forge groundingdino-py segment-anything-fast
 ```
 
 ## Examples

docs/examples/arcgis.ipynb

@@ -231,9 +231,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "sam.show_anns(axis=\"off\", alpha=1, output=\"ag_annotations.tif\")"
@@ -431,7 +429,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sam.generate('agriculture.tif', output=\"ag_masks2.tif\", foreground=True)"
+    "sam.generate(\"agriculture.tif\", output=\"ag_masks2.tif\", foreground=True)"
    ]
   },
   {

docs/examples/automatic_mask_generator_hq.ipynb

@@ -39,7 +39,13 @@
    "source": [
     "import os\n",
     "import leafmap\n",
-    "from samgeo.hq_sam import SamGeo, show_image, download_file, overlay_images, tms_to_geotiff"
+    "from samgeo.hq_sam import (\n",
+    "    SamGeo,\n",
+    "    show_image,\n",
+    "    download_file,\n",
+    "    overlay_images,\n",
+    "    tms_to_geotiff,\n",
+    ")"
    ]
   },
   {
@@ -147,7 +153,7 @@
    "outputs": [],
    "source": [
     "sam = SamGeo(\n",
-    "    model_type=\"vit_h\", # can be vit_h, vit_b, vit_l, vit_tiny\n",
+    "    model_type=\"vit_h\",  # can be vit_h, vit_b, vit_l, vit_tiny\n",
     "    sam_kwargs=None,\n",
     ")"
    ]
@@ -288,7 +294,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [

docs/examples/box_prompts.ipynb

@@ -241,7 +241,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "m.add_raster('mask.tif', cmap='viridis', nodata=0, layer_name='Mask')\n",
+    "m.add_raster(\"mask.tif\", cmap=\"viridis\", nodata=0, layer_name=\"Mask\")\n",
     "m"
    ]
   },
@@ -260,7 +260,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "url = 'https://opengeos.github.io/data/sam/tree_boxes.geojson'\n",
+    "url = \"https://opengeos.github.io/data/sam/tree_boxes.geojson\"\n",
     "geojson = \"tree_boxes.geojson\"\n",
     "leafmap.download_file(url, geojson)"
    ]
@@ -350,8 +350,7 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.10.8"
-  },
-  "orig_nbformat": 4
+  }
  },
  "nbformat": 4,
  "nbformat_minor": 2

docs/examples/fast_sam.ipynb

@@ -142,6 +142,7 @@
    "outputs": [],
    "source": [
     "from samgeo.fast_sam import SamGeo\n",
+    "\n",
     "sam = SamGeo(model=\"FastSAM-x.pt\")"
    ]
   },
@@ -259,8 +260,7 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.9.16"
-  },
-  "orig_nbformat": 4
+  }
  },
  "nbformat": 4,
  "nbformat_minor": 2

docs/examples/input_prompts.ipynb

@@ -37,7 +37,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -147,7 +147,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -260,8 +260,7 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.10.8"
-  },
-  "orig_nbformat": 4
+  }
  },
  "nbformat": 4,
  "nbformat_minor": 2

docs/examples/input_prompts_hq.ipynb

@@ -258,8 +258,7 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.9.16"
-  },
-  "orig_nbformat": 4
+  }
  },
  "nbformat": 4,
  "nbformat_minor": 2