Merge pull request #137 from XAITK/update-to-v0.7

Update to v0.7.

.github/workflows/ci-example-notebooks.yml

@@ -43,7 +43,7 @@ jobs:
 
     # Just one python version, using our base supported version.
     container:
-      image: python:3.7
+      image: python:3.8
       options: "--shm-size 2GB"
 
     # Steps represent a sequence of tasks that will be executed as part of the job
@@ -72,9 +72,9 @@ jobs:
             ~/.local
           # Using a different key due to additional things the notebook
           # examples ad-hoc install.
-          key: python-3.7-${{ hashFiles('poetry.lock') }}-Examples
+          key: python-3.8-${{ hashFiles('poetry.lock') }}-Examples
           restore-keys: |
-            python-3.7-${{ hashFiles('poetry.lock') }}
+            python-3.8-${{ hashFiles('poetry.lock') }}
 
       - name: Setup Environment
         # See: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#example-using-a-public-action-in-a-subdirectory
@@ -89,7 +89,7 @@ jobs:
           path: |
             ~/.cache/torch/
             examples/data/
-          key: python-3.7-${{ hashFiles('poetry.lock') }}-ExampleData-${{ matrix.notebook-file }}
+          key: python-3.8-${{ hashFiles('poetry.lock') }}-ExampleData-${{ matrix.notebook-file }}
           # pretty unique, no restore-keys.
 
       - name: Run Notebook

.github/workflows/ci-unittests.yml

@@ -28,7 +28,7 @@ defaults:
 jobs:
   lint:
     runs-on: ubuntu-latest
-    container: python:3.7
+    container: python:3.8
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
@@ -45,7 +45,7 @@ jobs:
           path: |
             ~/.cache/pypoetry/virtualenvs/
             ~/.local
-          key: python-3.7-${{ hashFiles('poetry.lock') }}
+          key: python-3.8-${{ hashFiles('poetry.lock') }}
       - name: Setup Environment
         # See: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#example-using-a-public-action-in-a-subdirectory
         uses: Kitware/SMQTK-Core/.github/actions/python-poetry-setup@master
@@ -54,7 +54,7 @@ jobs:
 
   typecheck:
     runs-on: ubuntu-latest
-    container: python:3.7
+    container: python:3.8
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
@@ -71,7 +71,7 @@ jobs:
           path: |
             ~/.cache/pypoetry/virtualenvs/
             ~/.local
-          key: python-3.7-${{ hashFiles('poetry.lock') }}
+          key: python-3.8-${{ hashFiles('poetry.lock') }}
       - name: Setup Environment
         # See: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#example-using-a-public-action-in-a-subdirectory
         uses: Kitware/SMQTK-Core/.github/actions/python-poetry-setup@master
@@ -82,7 +82,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.8","3.9","3.10","3.11"]
         # Extras for included, optional plugin support (space-separated lists)
         opt-extra: [
             "",  # no extras
@@ -128,8 +128,9 @@ jobs:
         run: poetry run pytest
 
       - name: CodeCov report submission
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true
           files: coverage.xml
           flags: unittests

.github/workflows/publish.yml

@@ -22,7 +22,7 @@ defaults:
 jobs:
   publish:
     runs-on: ubuntu-latest
-    container: python:3.7
+    container: python:3.8
     # This should only be run for tags on the "official" repository org.
     if: github.repository_owner == 'XAITK'
     steps:
@@ -41,7 +41,7 @@ jobs:
           path: |
             ~/.cache/pypoetry/virtualenvs/
             ~/.local
-          key: python-3.7-${{ hashFiles('poetry.lock') }}
+          key: python-3.8-${{ hashFiles('poetry.lock') }}
 
       - name: Setup Environment
         # Using non-relative path for correct behavior when used as a remote

.readthedocs.yaml

@@ -2,7 +2,7 @@ version: 2
 formats:
   - pdf
 python:
-  version: 3.7
+  version: 3.8
   install:
     - requirements: docs/readthedocs-reqs.txt
     - method: pip

docs/readthedocs-reqs.txt

@@ -1,2 +1,2 @@
 # Additional requirements for building our documentation in read-the-docs build
-sphinx-prompt==1.4.0
+sphinx-prompt

docs/release_notes.rst

@@ -11,3 +11,4 @@ Release Notes
    release_notes/v0.5.0
    release_notes/v0.6.0
    release_notes/v0.6.1
+   release_notes/v0.7.0

docs/release_notes/v0.7.0.rst

@@ -0,0 +1,44 @@
+v0.7.0
+======
+
+This minor release updates the mimumum supported python to `python = "^3.8"`, addresses dependency vulnerabilities, and updates typing to conform with current mypy and pytest standards.
+
+Updates / New Features
+----------------------
+
+Build
+
+* New minimum supported python changed to `python = "^3.8"`.
+
+CI
+
+* Updated codecov action version to 3.
+
+* Added explicit use of codecov token to facilitate successful coverage
+  submission.
+
+Dependencies
+
+* Updated ``notebook`` dependency due to a vulnerability alert.
+
+* Periodic update of locked dep versions within abstract version constraints.
+
+* Updated sphinx versions to fix local documentation building issue.
+
+* Updated python minimum requirement to 3.8 (up from 3.6). This involved a
+  number of updates and bifurcations of abstract requirements, an update to
+  pinned versions for development/CI, and expansion of CI to cover python
+  versions 3.10 and 3.11 (latest current release).
+
+Fixes
+-----
+
+Docs
+
+* Added missing step to the release process about creating the release on
+  GitHub's Releases section.
+
+Examples
+
+* Added a note to each example about restarting the runtime for compatibility
+  with Colab, as well as a step to create a data directory if necessary.

docs/release_process.rst

@@ -63,7 +63,9 @@ and functionalities.
       $ git merge --log --no-ff upstream/release
       $ git push upstream master
 
-7. Update version reference in the `XAITK/xaitk.github.io home page`_ to the
+8. `Draft a new release on GitHub`_ for the new version.
+
+9. Update version reference in the `XAITK/xaitk.github.io home page`_ to the
    new version.
 
 Patch Release
@@ -120,7 +122,9 @@ If a patch release for an older release version is being created, see the
       $ git merge --log --no-ff upstream/release
       $ git push upstream master
 
-8. If this patch release now represents the highest version of the package,
+8. `Draft a new release on GitHub`_ for the new version.
+
+9. If this patch release now represents the highest version of the package,
    update version reference in the `XAITK/xaitk.github.io home page`_ to the
    new version.
 
@@ -159,22 +163,33 @@ current package version.
 .. code-block:: bash
 
    $ git checkout HASH
-   # VERSION="v$(poetry version -s)"
+   $ VERSION="v$(poetry version -s)"
    $ git tag -a "$VERSION" -F docs/release_notes/"$VERSION".rst
    $ git push UPSTREAM "$VERSION"
 
+Draft a new release on Github
+-----------------------------
 After creating and pushing a new version tag, a GitHub "release" should be
 made.
-Navigate to the `releases page on GitHub`_ and click the ``Draft a new
-release`` button in the upper right.
-The newly added tag should be selected in the "Choose a tag" drop-down.
-The "Release Title" should be the version tag (i.e. "v#.#.#").
-Copy and paste this version's release notes into the ``Describe this release``
-text box.
-Remember to check the ``This is a pre-release`` check-box if appropriate.
-Click the ``Public release`` button at the bottom of the page when complete.
+
+a. Navigate to the GitHub `Releases page`_ for the xaitk-saliency repository.
+
+b. Click the "Draft a new release" button (or go `here
+   <https://github.com/XAITK/xaitk-saliency/releases/new>`_).
+
+c. Select from the "Choose a tag" drop down the tag version just created and
+   pushed
+
+d. Enter the version number as the title, e.g. "v1.2.3".
+
+e. Copy and paste the release notes for this version into the description
+   field.
+
+f. Select the "This is a pre-release" check-box if applicable.
+
+g. Click the "Publish Release" button to create the GitHub release!
 
 
 .. _Poetry's version command: https://python-poetry.org/docs/cli/#version
-.. _releases page on GitHub: https://github.com/XAITK/xaitk-saliency/releases
+.. _Releases page: https://github.com/XAITK/xaitk-saliency/releases
 .. _XAITK/xaitk.github.io home page: https://github.com/XAITK/xaitk.github.io/edit/master/_pages/home.md#L12

examples/DRISE.ipynb

@@ -41,7 +41,8 @@
    "id": "9db07c5f",
    "metadata": {},
    "source": [
-    "# Set Up Environment"
+    "# Set Up Environment\n",
+    "**Note for Colab users**: after setting up the environment, you may need to \"Restart Runtime\" in order to resolve package version conflicts (see the [README](https://github.com/XAITK/xaitk-saliency/blob/master/examples/README.md#run-the-notebooks-from-colab) for more info)."
    ]
   },
   {
@@ -102,6 +103,7 @@
     }
    ],
    "source": [
+    "import os\n",
     "import PIL.Image\n",
     "import matplotlib.pyplot as plt\n",
     "import urllib.request\n",
@@ -112,6 +114,7 @@
     "\n",
     "\n",
     "# Test image to be explained\n",
+    "os.makedirs('data', exist_ok=True)\n",
     "test_image_filename = 'data/catdog.jpg'\n",
     "urllib.request.urlretrieve('https://farm1.staticflickr.com/74/202734059_fcce636dcd_z.jpg', test_image_filename)\n",
     "plt.figure(figsize=(12, 8))\n",
@@ -255,7 +258,7 @@
     "blackbox_detector = ResNetFRCNN(\n",
     "    box_thresh=0.05,\n",
     "    img_batch_size=1,\n",
-    "    use_cuda=True\n",
+    "    use_cuda=False\n",
     ")\n",
     "\n",
     "model_mean = [0.485, 0.456, 0.406]\n",

examples/MNIST_scikit_saliency.ipynb

@@ -57,7 +57,8 @@
    },
    "source": [
     "# MNIST Dataset Example <a name=\"MNIST-Dataset-Example-mnist\"></a>\n",
-    "## Set Up Environment <a name=\"Set-Up-Environment-mnist\"></a>"
+    "## Set Up Environment <a name=\"Set-Up-Environment-mnist\"></a>\n",
+    "**Note for Colab users**: after setting up the environment, you may need to \"Restart Runtime\" in order to resolve package version conflicts (see the [README](https://github.com/XAITK/xaitk-saliency/blob/master/examples/README.md#run-the-notebooks-from-colab) for more info)."
    ]
   },
   {

examples/ModelComparisonWithSaliency.ipynb

@@ -27,7 +27,9 @@
    "source": [
     "## Setup Environment\n",
     "\n",
-    "Here we install `xaitk-saliency` and the \"centernet\" extra for `smqtk-detection` which includes the dependencies for the PyTorch-based `CenterNetVisdrone` class."
+    "Here we install `xaitk-saliency` and the \"centernet\" extra for `smqtk-detection` which includes the dependencies for the PyTorch-based `CenterNetVisdrone` class.\n",
+    "\n",
+    "**Note for Colab users**: after setting up the environment, you may need to \"Restart Runtime\" in order to resolve package version conflicts (see the [README](https://github.com/XAITK/xaitk-saliency/blob/master/examples/README.md#run-the-notebooks-from-colab) for more info)."
    ]
   },
   {
@@ -404,7 +406,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "import urllib\n",
     "\n",
     "from smqtk_detection.impls.detect_image_objects.centernet import CenterNetVisdrone\n",

examples/Radial_Image_Perturbation.ipynb

@@ -18,19 +18,30 @@
     "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/XAITK/xaitk-saliency/blob/master/examples/Radial_Image_Perturbation.ipynb)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "9f91a2fd",
+   "metadata": {},
+   "source": [
+    "# Set Up Environment\n",
+    "**Note for Colab users**: after setting up the environment, you may need to \"Restart Runtime\" in order to resolve package version conflicts (see the [README](https://github.com/XAITK/xaitk-saliency/blob/master/examples/README.md#run-the-notebooks-from-colab) for more info)."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
    "id": "f129287c",
    "metadata": {},
    "outputs": [],
    "source": [
+    "import os\n",
     "import sys\n",
     "# Python dependencies\n",
     "!{sys.executable} -m pip install -qU pip\n",
     "!{sys.executable} -m pip install -q xaitk-saliency\n",
     "\n",
     "# Data dependencies\n",
+    "os.makedirs('data', exist_ok=True)\n",
     "image_filepath = \"data/Grace_Hopper.jpg\"\n",
     "![ ! -f \"{image_filepath}\" ] && wget https://upload.wikimedia.org/wikipedia/commons/5/55/Grace_Hopper.jpg -O {image_filepath}"
    ]