Merge branch 'master' into test-pilot

Author: hainm

.github/nglview-gha.yml

@@ -4,8 +4,6 @@ channels:
   - conda-forge
 
 dependencies:
-  - python>=3.6
-  - pip
   - jupyter-packaging
   - qcelemental
   - traitlets
@@ -15,15 +13,12 @@ dependencies:
   - notebook
   - mock
   - coverage
-  - nose
   - pytest
   - pytest-cov
-  - coveralls
   - pandas
   - ase
   - biopython
   - pymatgen
-  - simpletraj
   - matplotlib
   - moviepy
   - imageio
@@ -32,5 +27,9 @@ dependencies:
   - rdkit
   - mdanalysis
   - mdtraj
-  - parmed
-  - ambertools
+  - ambertools # have both pytraj and parmed
+  - pip
+  - pip:
+    - simpletraj
+
+

.github/workflows/build-extension.yml

@@ -17,7 +17,7 @@ jobs:
     - name: Install node
       uses: actions/setup-node@v1
       with:
-       node-version: '16.x'
+       node-version: '20.x'
     - name: Install Python
       uses: actions/setup-python@v2
       with:

.github/workflows/test.yml

@@ -16,14 +16,14 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.9]
+        python-version: [3.9, 3.11, 3.12]
 
     steps:
     - name: Checkout nglview repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Cache conda
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       env:
         CACHE_NUMBER: 2  # Increase this value to reset cache if .github/nglview-gha.yml has not changed
       with:
@@ -32,7 +32,7 @@ jobs:
           ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/nglview-gha.yml') }}
 
     - name: Set up conda environment
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
         auto-activate-base: false
@@ -52,4 +52,4 @@ jobs:
       run: |
         python setup.py sdist
         pip install dist/*gz
-        python -c "import nglview as nv; print(nv.__version__)"
+        python -c "import nglview as nv; print(nv.__version__)"

binder/environment.yml

@@ -0,0 +1,6 @@
+module.exports = {
+    files: ["**/*.ts"],
+    languageOptions: {
+        parser: require('@typescript-eslint/parser'), // Specifies the ESLint parser
+    }
+};

binder/postBuild

@@ -45,8 +45,8 @@
     "clean:lib": "rimraf lib tsconfig.tsbuildinfo",
     "clean:labextension": "rimraf myextension/labextension",
     "clean:all": "yarn run clean:lib && yarn run clean:labextension",
-    "eslint": "eslint . --ext .ts,.tsx --fix",
-    "eslint:check": "eslint . --ext .ts,.tsx",
+    "eslint": "eslint '**/*.ts' --fix",
+    "eslint:check": "eslint '**/*.ts'",
     "install:extension": "jupyter labextension develop --overwrite .",
     "prepare": "yarn run clean && yarn run build:prod",
     "watch": "run-p watch:src watch:labextension",
@@ -70,11 +70,11 @@
     "@types/mocha": "^2.2.48",
     "@types/node": "^16.0.0",
     "@types/requirejs": "^2.1.31",
-    "@typescript-eslint/eslint-plugin": "^4.8.1",
-    "@typescript-eslint/parser": "^4.8.1",
+    "@typescript-eslint/eslint-plugin": "^7.13.1",
+    "@typescript-eslint/parser": "^7.13.1",
     "babel-register": "^6.11.6",
     "css-loader": "^0.23.1",
-    "eslint": "^7.14.0",
+    "eslint": "^8.5.6",
     "file-loader": "^1.1.6",
     "json-loader": "^0.5.4",
     "mkdirp": "^1.0.3",
@@ -83,7 +83,7 @@
     "prettier": "^2.1.1",
     "rimraf": "^3.0.2",
     "style-loader": "^0.13.1",
-    "typescript": "~4.1.3",
+    "typescript": "~5.4.5",
     "webpack": "^3.12.0"
   },
   "sideEffects": [

binder/runtime.txt

@@ -84,7 +84,7 @@ if (window.require) {
 module.exports = {
     load_ipython_extension: function () { }
 };
-//# sourceMappingURL=data:application/json;base64,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
+//# sourceMappingURL=data:application/json;base64,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
 
 /***/ })
 /******/ ])});;

js/.eslintignore

@@ -45,8 +45,8 @@
     "clean:lib": "rimraf lib tsconfig.tsbuildinfo",
     "clean:labextension": "rimraf myextension/labextension",
     "clean:all": "yarn run clean:lib && yarn run clean:labextension",
-    "eslint": "eslint . --ext .ts,.tsx --fix",
-    "eslint:check": "eslint . --ext .ts,.tsx",
+    "eslint": "eslint '**/*.ts' --fix",
+    "eslint:check": "eslint '**/*.ts'",
     "install:extension": "jupyter labextension develop --overwrite .",
     "prepare": "yarn run clean && yarn run build:prod",
     "watch": "run-p watch:src watch:labextension",
@@ -70,11 +70,11 @@
     "@types/mocha": "^2.2.48",
     "@types/node": "^16.0.0",
     "@types/requirejs": "^2.1.31",
-    "@typescript-eslint/eslint-plugin": "^4.8.1",
-    "@typescript-eslint/parser": "^4.8.1",
+    "@typescript-eslint/eslint-plugin": "^7.13.1",
+    "@typescript-eslint/parser": "^7.13.1",
     "babel-register": "^6.11.6",
     "css-loader": "^0.23.1",
-    "eslint": "^7.14.0",
+    "eslint": "^8.5.6",
     "file-loader": "^1.1.6",
     "json-loader": "^0.5.4",
     "mkdirp": "^1.0.3",
@@ -83,7 +83,7 @@
     "prettier": "^2.1.1",
     "rimraf": "^3.0.2",
     "style-loader": "^0.13.1",
-    "typescript": "~4.1.3",
+    "typescript": "~5.4.5",
     "webpack": "^3.12.0"
   },
   "sideEffects": [
@@ -101,7 +101,7 @@
       }
     },
     "_build": {
-      "load": "static/remoteEntry.21d0885d0060a84340da.js",
+      "load": "static/remoteEntry.4aa080b2a45dbecd0a13.js",
       "extension": "./extension",
       "style": "./style"
     }

js/.eslintrc

@@ -8,7 +8,7 @@
     },
     {
       "name": "css-loader",
-      "versionInfo": "6.9.0",
+      "versionInfo": "6.11.0",
       "licenseId": "MIT",
       "extractedText": "Copyright JS Foundation and other contributors\n\nPermission is hereby granted, free of charge, to any person obtaining\na copy of this software and associated documentation files (the\n'Software'), to deal in the Software without restriction, including\nwithout limitation the rights to use, copy, modify, merge, publish,\ndistribute, sublicense, and/or sell copies of the Software, and to\npermit persons to whom the Software is furnished to do so, subject to\nthe following conditions:\n\nThe above copyright notice and this permission notice shall be\nincluded in all copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,\nEXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF\nMERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.\nIN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY\nCLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,\nTORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE\nSOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n"
     },
@@ -20,9 +20,9 @@
     },
     {
       "name": "jquery-ui",
-      "versionInfo": "1.13.2",
+      "versionInfo": "1.13.3",
       "licenseId": "MIT",
-      "extractedText": "Copyright jQuery Foundation and other contributors, https://jquery.org/\n\nThis software consists of voluntary contributions made by many\nindividuals. For exact contribution history, see the revision history\navailable at https://github.com/jquery/jquery-ui\n\nThe following license applies to all parts of this software except as\ndocumented below:\n\n====\n\nPermission is hereby granted, free of charge, to any person obtaining\na copy of this software and associated documentation files (the\n\"Software\"), to deal in the Software without restriction, including\nwithout limitation the rights to use, copy, modify, merge, publish,\ndistribute, sublicense, and/or sell copies of the Software, and to\npermit persons to whom the Software is furnished to do so, subject to\nthe following conditions:\n\nThe above copyright notice and this permission notice shall be\nincluded in all copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND,\nEXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF\nMERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND\nNONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE\nLIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION\nOF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION\nWITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n\n====\n\nCopyright and related rights for sample code are waived via CC0. Sample\ncode is defined as all source code contained within the demos directory.\n\nCC0: http://creativecommons.org/publicdomain/zero/1.0/\n\n====\n\nAll files located in the node_modules and external directories are\nexternally maintained libraries used by this software which have their\nown licenses; we recommend you read them, as their terms may differ from\nthe terms above.\n"
+      "extractedText": "Copyright OpenJS Foundation and other contributors, https://openjsf.org/\n\nThis software consists of voluntary contributions made by many\nindividuals. For exact contribution history, see the revision history\navailable at https://github.com/jquery/jquery-ui\n\nThe following license applies to all parts of this software except as\ndocumented below:\n\n====\n\nPermission is hereby granted, free of charge, to any person obtaining\na copy of this software and associated documentation files (the\n\"Software\"), to deal in the Software without restriction, including\nwithout limitation the rights to use, copy, modify, merge, publish,\ndistribute, sublicense, and/or sell copies of the Software, and to\npermit persons to whom the Software is furnished to do so, subject to\nthe following conditions:\n\nThe above copyright notice and this permission notice shall be\nincluded in all copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND,\nEXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF\nMERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND\nNONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE\nLIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION\nOF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION\nWITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n\n====\n\nCopyright and related rights for sample code are waived via CC0. Sample\ncode is defined as all source code contained within the demos directory.\n\nCC0: http://creativecommons.org/publicdomain/zero/1.0/\n\n====\n\nAll files located in the node_modules and external directories are\nexternally maintained libraries used by this software which have their\nown licenses; we recommend you read them, as their terms may differ from\nthe terms above.\n"
     },
     {
       "name": "ngl",

js/eslint.config.js

@@ -16,12 +16,6 @@
     create_cmdclass,
 )
 
-import versioneer
-from versioneer import get_cmdclass
-
-sdist = get_cmdclass()['sdist']
-build_py = get_cmdclass()['build_py']
-
 here = os.path.dirname(os.path.abspath(__file__))
 node_root = os.path.join(here, 'js')
 is_repo = os.path.exists(os.path.join(here, '.git'))
@@ -151,14 +145,12 @@ def run(self):
     data_files_spec=data_files_spec
 )
 cmdclass['jsdeps'] = NPM
-cmdclass['version'] = get_cmdclass()['version']
-cmdclass['build_py'] = js_prerelease(build_py)
-cmdclass['sdist'] = js_prerelease(sdist, strict=True)
 cmdclass['egg_info'] = js_prerelease(egg_info)
 
 setup_args = {
     'name': 'nglview',
-    'version': versioneer.get_version(),
+    "use_scm_version": True,
+    "setup_requires": ['setuptools_scm'],
     'description': 'IPython widget to interactively view molecular structures and trajectories.',
     'include_package_data': True,
     'license': "MIT",
@@ -196,7 +188,7 @@ def run(self):
         "htmd": ["htmd"],
         "qcelemental": ["qcelemental"],
     },
-    'packages': set(find_packages() + 
+    'packages': set(find_packages() +
                 ['nglview',
                  'nglview.static',
                  'nglview.staticlab',