build: add pip dependencies

.github/workflows/conda_build_and_publish.yml

@@ -1,27 +1,21 @@
-name: conda_build
-
+name: conda
 on:
-  release:
-    types: [published]
-  push:
-    branches: [ master ]
-    tags:
-      - '**'
-  pull_request:
-    branches: [ master ]
-
+  release: {types: [published]}
+  push: {branches: [master], tags: ['**']}
+  pull_request: {branches: [master]}
 jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - name: publish-to-conda
-      uses: paskino/conda-package-publish-action@v1.4.4
+    - uses: actions/checkout@v4
       with:
-        subDir: 'recipe'
+        fetch-depth: 0
+        ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA
+    - uses: TomographicImaging/conda-package-publish-action@v2
+      with:
+        additional_apt_packages: libgl-dev
+        subDir: recipe
         channels: '-c conda-forge -c ccpi -c paskino'
         AnacondaToken: ${{ secrets.ANACONDA_TOKEN }}
         publish: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') }}
         test_all: ${{(github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')) || (github.ref == 'refs/heads/master')}}
-        convert_win: false
-        convert_osx: false

.github/workflows/docs_build_and_publish.yml

@@ -1,3 +1,4 @@
+name: docs
 on:
   release:
     types: [published]
@@ -13,13 +14,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - uses: ammaraskar/sphinx-action@master
       with:
         docs-folder: "docs/"
         pre-build-command: python -m pip install --upgrade pip; pip install sphinx_rtd_theme
     # Create an artifact of the html output.
-    - uses: actions/upload-artifact@v1
+    - uses: actions/upload-artifact@v4
       with:
         name: DocumentationHTML
         path: docs/build/html/
@@ -30,7 +31,7 @@ jobs:
     if: github.ref == 'refs/heads/master'
     steps:
     - name: Download artifact of the html output.
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: DocumentationHTML
         path: docs/build/html/

CHANGES.md

@@ -1,11 +1,13 @@
 # ChangeLog
 
 ## vx.x.x
-* Add automatic registration functionality
-* Set empty pop-up menus for the main windows
-* Set Tabified widgets not to move or close
-* Set QDockWidgets flag to NoDockWidgetFeatures to prevent them being moved or lost
-* Consume events 'w' and 's' in viewers to avoid render changes between wireframe and surface respectively
+* fix some missing pip dependencies & update workflows & fix tests #233
+* Edit registration-tab name from "Manual" to "Initial" #241
+* Add automatic registration functionality #304
+* Set empty pop-up menus for the main windows #217
+* Set Tabified widgets not to move or close #226 #217
+* Set QDockWidgets flag to NoDockWidgetFeatures to prevent them being moved or lost #226 #217
+* Consume events 'w' and 's' in viewers to avoid render changes between wireframe and surface respectively #218
 * Added argument parser to idvc command. This allows the user to specify the debugging level
 * Add workaround for box clipping due to VTK behaviour change from 9.1. Removed requirement for VTK 8.1.2
 * add build directory to gitignore

recipe/meta.yaml

@@ -6,13 +6,11 @@ source:
   path: ../
 
 build:
-  number: {{ GIT_DESCRIBE_NUMBER }}
+  number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
   noarch: python
   preserve_egg_dir: False
-
   entry_points:
     - idvc = idvc.idvc:main
-
   missing_dso_whitelist:
     - /lib64/libc.so.6            # [linux]
     - /lib64/libm.so.6            # [linux]
@@ -23,22 +21,18 @@ build:
     - C:\Windows\System32\msvcrt.dll   # [win]
     - C:\Windows\System32\SHELL32.dll  # [win]
 
-
 test:
   source_files:
     - ./test
-
   commands:
-    - python -c "import os; print ('TESTING IN THIS DIRECTORY' , os.getcwd())"
+    - python -c "import os; print('TESTING IN THIS DIRECTORY', os.getcwd())"
     - python -m unittest discover test
-  
+
 requirements:
-
   build:
     - python
     - numpy
     - typing_extensions # [py<=37]
-
   run:
     - python
     - numpy

setup.py

@@ -20,7 +20,7 @@
 
 def version2pep440(version):
     '''normalises the version from git describe to pep440
-    
+
     https://www.python.org/dev/peps/pep-0440/#id29
     '''
     if version[0] == 'v':
@@ -55,12 +55,22 @@ def version2pep440(version):
     f.write('version = \'{}\''.format(dversion))
 
 setup(
-      name = "idvc",
-      description = 'CCPi DVC Configurator',
-	  version = dversion,
-	  packages = {'idvc', 'idvc.ui', 'idvc.utils'},
-      package_dir = {'idvc': os.path.join('src','idvc')},
-      package_data = {'idvc':['DVCIconSquare.png']},
+      name="idvc",
+      description='CCPi DVC Configurator',
+	  version=dversion,
+	  packages={'idvc', 'idvc.ui', 'idvc.utils'},
+      package_dir={'idvc': os.path.join('src','idvc')},
+      package_data={'idvc':['DVCIconSquare.png']},
+      install_requires=[
+        "scipy",
+        # "ccpi-viewer>=22.2.0", # TODO: put on pypi
+        "natsort",
+        "docopt",
+        "matplotlib",
+        # "openmp; platform_system=='Darwin'",
+        "qdarkstyle",
+        "vtk",
+      ],
       # metadata for upload to PyPI
       author="Edoardo Pasca, Laura Murgatroyd",
       author_email="edo.paskino@gmail.com",

src/idvc/__init__.py

@@ -12,3 +12,7 @@
 
 #   Author: Laura Murgatroyd (UKRI-STFC)
 #   Author: Edoardo Pasca (UKRI-STFC)
+try:
+    import ccpi.viewer
+except ImportError as exc:
+    raise ImportError('Please `conda install "ccpi::ccpi-viewer>=22.2.0"`') from exc

src/idvc/dvc_interface.py

@@ -1042,7 +1042,7 @@ def setup3DPointCloudPipeline(self):
     def CreateRegistrationPanel(self):
         """Create the Registration Dockable Widget"""
 
-        self.registration_panel = generateUIDockParameters(self, '2 - Manual Registration')
+        self.registration_panel = generateUIDockParameters(self, '2 - Initial Registration')
         dockWidget = self.registration_panel[0]
         dockWidget.setObjectName("RegistrationPanel")
         groupBox = self.registration_panel[5]
@@ -1739,7 +1739,7 @@ def LoadCorrImageForReg(self,resample_corr_image= False, crop_corr_image = False
                                          crop_image=crop_corr_image, origin=origin, target_z_extent=z_extent, finish_fn=self.completeRegistration, output_dir=os.path.abspath(tempfile.tempdir))
 
     def completeRegistration(self):
-        """It shows the registration difference volume in the viewer and sets up the tab for the manual registration. 
+        """It shows the registration difference volume in the viewer and sets up the tab for the registration. 
         It runs the automatic registration and shows the results and the extra buttons."""
         self.manualRegistration()
         automatic_reg_worker = Worker(self.automatic_reg_run)
@@ -1937,7 +1937,7 @@ def reg_viewer_update(self, type = None):
         type : str
             If 'starting registration' then the registration viewer is centred on the slice that contains point 0.
             This is the case if the "Start Registration" button is pressed. Otherwise, when type=None we are in the middle of 
-            manual registration and the viewer is centred on the current slice
+            registration and the viewer is centred on the current slice
             If 'manual registration' then the translation widgets are updated with the current translation on each axis.
             If 'automatic registration' then the translation widgets are not updated.
         '''