Merge pull request #150 from DiamondLightSource/removecucim

dkazanc · web-flow · commit 7ae56bde0c57 · 2024-08-27T14:12:16.000+01:00
retiring cucim dependency
diff --git a/.github/workflows/httomolibgpu_doc_conda.yml b/.github/workflows/httomolibgpu_doc_conda.yml
@@ -1,4 +1,4 @@
-name: HTTomolibGPU doc test
+name: HTTomolibgpu docs
 
 on:
   workflow_dispatch:
@@ -24,7 +24,7 @@ jobs:
           with:
             python-version: "3.10"
 
-        - name: httomolibgpu
+        - name: httomolib
           uses: conda-incubator/setup-miniconda@v2
           with:
             auto-update-conda: false
@@ -40,4 +40,5 @@ jobs:
         - name: Run ghp-import
           run: ghp-import -n -p -f ./docs/build
           env:
-            GITHUB_TOKEN: ${{ github.token }}
+            GITHUB_TOKEN: ${{ github.token }}            
+          
diff --git a/.github/workflows/httomolibgpu_nightly_build.yml b/.github/workflows/httomolibgpu_nightly_build.yml
@@ -1,12 +1,12 @@
-name: httomolibgpu nightly dev conda package build + upload
+name: httomolibgpu nightly dev
 
 on:
   schedule:
     # Run at midnight every day
     - cron: '0 0 * * *'
 
 jobs:
-  build-linux:
+  main-conda-build:
     runs-on: ubuntu-20.04
 
     defaults:
@@ -20,11 +20,11 @@ jobs:
           ref: "main"
           fetch-depth: 0
 
-      # setup Python 3.9
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v2
+      # setup Python 3.10
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       - name: Decrypt a secret
         run: ./.scripts/decrypt_secret.sh
diff --git a/.github/workflows/httomolibgpu_tests_run_iris.yml b/.github/workflows/httomolibgpu_tests_run_iris.yml
@@ -1,5 +1,4 @@
-name: httomolibgpu tests on Iris
-
+name: httomolibgpu tests
 on:
   push:
     branches:
@@ -9,7 +8,7 @@ on:
       - main
 
 jobs:
-  build-linux:
+  iris-gpu:
     runs-on: iris-gpu
     container:
       image: nvidia/cuda:11.6.2-devel-ubi8
diff --git a/.github/workflows/httomolibgpu_version_tag.yml b/.github/workflows/httomolibgpu_version_tag.yml
@@ -1,4 +1,4 @@
-name: httomolibgpu conda upload
+name: httomolibgpu version tag pushed
 
 # Run the workflow whenever a tag beginning with `v` is pushed to any branch
 on:
@@ -7,7 +7,7 @@ on:
       - v*
 
 jobs:
-  build-linux:
+  conda-upload-main:
     runs-on: ubuntu-20.04
 
     defaults:
@@ -21,11 +21,11 @@ jobs:
           fetch-depth: 0
           ref: ${{ github.ref_name }}
 
-      # setup Python 3.9
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v2
+      # setup Python 3.10
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       # install dependencies with conda
       - name: Install dependencies with conda
diff --git a/.scripts/conda_upload.sh b/.scripts/conda_upload.sh
@@ -13,7 +13,7 @@ export CONDA_BLD_PATH=~/conda-bld
 $CONDA/bin/conda install conda-build
 $CONDA/bin/conda install -c conda-forge anaconda-client
 
-$CONDA/bin/conda build . -c conda-forge -c httomo -c rapidsai --no-test
+$CONDA/bin/conda build . -c conda-forge -c httomo --no-test
 
 # upload packages to conda
 find $CONDA_BLD_PATH/$OS -name *.tar.bz2 | while read file
diff --git a/LICENSE b/LICENSE
@@ -1,32 +1,32 @@
-HTTomoLibGPU is dual licenced under the Apache V2 and GPL V3 licences both of 
-which appear bellow.  The following section from the apache website
-details the compatability of ApacheV2 with GPLV3 and explains the 
+HTTomoLibGPU is dual licenced under the Apache V2 and GPL V3 licences both of
+which appear below. The following section from the apache website
+details the compatibility of ApacheV2 with GPLV3 and explains the
 requirement for the dual licence.
 
 
       From http://www.apache.org/licenses/GPL-compatibility.html
 
-The Free Software Foundation considers the Apache License, Version 
+The Free Software Foundation considers the Apache License, Version
 2.0 to be a free software license, compatible with version 3 of the GPL.
-The Software Freedom Law Center provides practical advice for developers 
+The Software Freedom Law Center provides practical advice for developers
 about including permissively licensed source.
 
-Apache 2 software can therefore be included in GPLv3 projects, because 
-the GPLv3 license accepts our software into GPLv3 works. However, GPLv3 
-software cannot be included in Apache projects. The licenses are incompatible 
-in one direction only, and it is a result of ASF's licensing philosophy and 
+Apache 2 software can therefore be included in GPLv3 projects, because
+the GPLv3 license accepts our software into GPLv3 works. However, GPLv3
+software cannot be included in Apache projects. The licenses are incompatible
+in one direction only, and it is a result of ASF's licensing philosophy and
 the GPLv3 authors' interpretation of copyright law.
 
-This licensing incompatibility applies only when some Apache project software 
-becomes a derivative work of some GPLv3 software, because then the Apache 
-software would have to be distributed under GPLv3. This would be incompatible 
-with ASF's requirement that all Apache software must be distributed under the 
+This licensing incompatibility applies only when some Apache project software
+becomes a derivative work of some GPLv3 software, because then the Apache
+software would have to be distributed under GPLv3. This would be incompatible
+with ASF's requirement that all Apache software must be distributed under the
 Apache License 2.0.
 
-We avoid GPLv3 software because merely linking to it is considered by the GPLv3 
-authors to create a derivative work. We want to honor their license. Unless GPLv3 
-licensors relax this interpretation of their own license regarding linking, our 
-licensing philosophies are fundamentally incompatible. This is an identical issue 
+We avoid GPLv3 software because merely linking to it is considered by the GPLv3
+authors to create a derivative work. We want to honor their license. Unless GPLv3
+licensors relax this interpretation of their own license regarding linking, our
+licensing philosophies are fundamentally incompatible. This is an identical issue
 for both GPLv2 and GPLv3.
 
 
@@ -36,9 +36,9 @@ for both GPLv2 and GPLv3.
 HTTomoLibGPU makes use of some GPLv3 libraries in the following packages:
     ToMoBAR (depends on ASTRA-Toolbox)
 
-If your use of the code makes use of these imports, then the software is licenced under 
+If your use of the code makes use of these imports, then the software is licenced under
 GPLV3 as required by the licence.  However if you do not use or redistribute the plugins
-containing these imports, the software may be considered licenced under the Apache V2 
+containing these imports, the software may be considered licenced under the Apache V2
 licence, Specifically all of the core functionality of HTTomoLibGPU.
 
 Both licences now follow.
diff --git a/README.rst b/README.rst
@@ -20,9 +20,7 @@ Install HTTomolibGPU as a pre-built conda Python package
 
    $ conda create --name httomolibgpu # create a fresh conda environment
    $ conda activate httomolibgpu # activate the environment
-   $ conda install -c httomo httomolibgpu -c rapidsai -c conda-forge # for linux users
-   $ conda install -c httomo httomolibgpu -c jplumail -c conda-forge # for windows users
-
+   $ conda install -c httomo httomolibgpu -c conda-forge # for linux users
 
 Setup the development environment:
 ==================================
@@ -39,5 +37,5 @@ Build HTTomolibGPU as a conda Python package
 
 .. code-block:: console
 
-   $ conda build conda/recipe/ -c conda-forge -c httomo -c rapidsai
+   $ conda build conda/recipe/ -c conda-forge -c httomo
 
diff --git a/conda/environment.yml b/conda/environment.yml
@@ -2,7 +2,6 @@ name: httomolibgpu
 channels:
   - conda-forge
   - httomo
-  - rapidsai
 dependencies:
   - conda-forge::cupy=12.3.0
   - conda-forge::numpy<=1.25
@@ -21,5 +20,4 @@ dependencies:
   - conda-forge::h5py
   - conda-forge::astra-toolbox
   - httomo::tomobar
-  - rapidsai::cucim
   - conda-forge::scikit-image
diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
@@ -24,7 +24,6 @@ requirements:
     - python
     - numpy>= 1.20, <= 1.25
     - cupy=12.3.0
-    - cucim
     - astra-toolbox
     - nvtx
     - tomobar
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -32,10 +32,12 @@
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = mock.Mock()
 
+
 class CustomMock(mock.Mock):
     def __repr__(self):
         return "<cp.ndarray>"
 
+
 sys.modules["cupy"] = CustomMock()
 sys.modules["numpy"] = CustomMock()
 
@@ -95,14 +97,6 @@ def __repr__(self):
 html_static_path = ["_static"]
 html_use_smartypants = True
 
-"""
-html_theme_options = {
-    "logo_only": True,
-    "display_version": False,
-    "githuburl": "https://github.com/DiamondLightSource/httomolibgpu",
-}
-"""
-
 html_theme_options = {
     "show_toc_level": 1,
     "navbar_align": "left",  # [left, content, right] For testing that the navbar items align properly
diff --git a/docs/source/scripts/methods_to_generate_images.py b/docs/source/scripts/methods_to_generate_images.py
@@ -118,7 +118,7 @@ def run_methods(path_to_data: str, output_folder: str) -> int:
         cp.asarray(proj_raw), cp.asarray(flats), cp.asarray(darks), minus_log=True
     )
     data_normalized_np = data_normalized.get()
-    
+
     max_scale_data_normalized = np.max(data_normalized_np)
     min_scale_data_normalized = np.min(data_normalized_np)
     assert max_scale_data_normalized > 1.062
@@ -168,7 +168,7 @@ def run_methods(path_to_data: str, output_folder: str) -> int:
         slice_numb=slice_numb,
     )
     del res_cp, res_np, proj_raw_mod
-    
+
     ## %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     methods_name = "median_filter"
     print("___{}___".format(methods_name))
@@ -182,7 +182,7 @@ def run_methods(path_to_data: str, output_folder: str) -> int:
         axis=None,
     )
     res_np = res_cp.get()
-    
+
     __save_res_to_image(
         res_np,
         output_folder,
@@ -197,9 +197,9 @@ def run_methods(path_to_data: str, output_folder: str) -> int:
         methods_name=methods_name + "_res",
         slice_numb=slice_numb,
         max_scale=0.05,
-        min_scale=0,        
+        min_scale=0,
     )
-    del res_cp, res_np    
+    del res_cp, res_np
 
     return 0
 
diff --git a/httomolibgpu/misc/corr.py b/httomolibgpu/misc/corr.py
diff --git a/httomolibgpu/recon/rotation.py b/httomolibgpu/recon/rotation.py
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/tests/test_misc/test_corr.py b/tests/test_misc/test_corr.py
diff --git a/tests/test_misc/test_morph.py b/tests/test_misc/test_morph.py
