Merge pull request #26 from fangohr/repo2docker-container-tests

Repo2docker container tests

Author: fangohr

.github/workflows/binder-nbval.yml

@@ -0,0 +1,27 @@
+name: NBVAL on binder container
+
+# We use `repo2docker` to build the docker image. Same as would happen on myBinder (or other Binder instances)
+
+on:
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  repo2docker-build-and-test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build Docker Container with repo2docker
+      uses: jupyterhub/repo2docker-action@master
+      with:
+        NO_PUSH: 'true'
+        IMAGE_NAME: "python4compscience"
+
+    - name: List Available Images
+      run: docker images
+
+    - name: Test with nbval
+      run: make docker-binder-nbval
+

.github/workflows/stage.yml

@@ -56,15 +56,15 @@ jobs:
 #       env:
 #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 #         NETLIFY_DIR: ./book/_build/html
-# 
+#
 #     - name: Publish Staging Site
 #       id: netlify-deploy
 #       uses: netlify/actions/cli@6c34c3fcafc69ac2e1d6dbf226560329c6dfc51b
 #       with:
 #         args: deploy --dir=./book/_build/html
 #       env:
 #         NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY }}
-# 
+#
 #     - uses: mshick/add-pr-comment@07f690343c25a94e24a8acb70d03c86b701ae322
 #       with:
 #         message: ${{ steps.netlify-deploy.outputs.NETLIFY_OUTPUT }}

Makefile

@@ -29,6 +29,13 @@ nbval:
 	pytest -v --nbval-lax book/18-environments.ipynb
 
 
+nbval-native:
+	@echo "Testing all chapters (apart from 18) with --nbval"
+	pytest -v --nbval book --sanitize-with book/static/nbval_sanitize.cfg \
+	    --ignore=book/18-environments.ipynb --ignore=book/_build
+	@echo "Testing chapter 18 with --nbval-lax"
+	pytest -v --nbval-lax book/18-environments.ipynb
+
 
 docker-all:
 	make docker-build
@@ -66,6 +73,9 @@ docker-nbval:
 docker-clean:
 	$(DOCKER_RUN) make clean
 
+docker-binder-nbval:
+	$(DOCKER_RUN) make nbval-native
+
 # to update the title page:
 # - screenshot first page of pdf
 # - (edit out date if desired)

Readme.md

@@ -2,6 +2,7 @@
 <!-- markdown-link-check-disable -->
 <!-- TODO: Enable this AFTER first merge and deploy to master! -->
 ![Book Deploy](https://github.com/fangohr/introduction-to-python-for-computational-science-and-engineering/workflows/Book%20Deploy/badge.svg)
+[![nbval in repo2docker container](https://github.com/fangohr/introduction-to-python-for-computational-science-and-engineering/actions/workflows/binder-nbval.yml/badge.svg)](https://github.com/fangohr/introduction-to-python-for-computational-science-and-engineering/actions/workflows/binder-nbval.yml)
 <!-- markdown-link-check-enable -->
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1411868.svg)](https://doi.org/10.5281/zenodo.1411868)
 [![License: CC BY-NC 4.0](https://img.shields.io/badge/License-CC%20BY--NC%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc/4.0/)

binder/info.org

@@ -12,19 +12,3 @@ leaner definition of dependencies.
 Binder should look in this directory (as it is called 'binder') and ignore the
 global Dockerfile.
 
-* Re-use dependencies from development environment in myBinder
-
-I don't know if myBinder could read dependencies from a pyproject.toml file (and
-couldn't find any documentation on this yet), nor if we can extract a
-requirements.txt file from the pyproject.toml file automatically.
-
-As a first step towards making the binder image leaner, I will stick to a definition via a Dockerfile, and leave out latex to make it smaller.
-
-This didn't go so well.
-
-Next attempt: specifying the packages we need in requirements.txt directly. It's
-not ideal, as we don't run tests on the particular versions, and we duplicate
-some effort from ../pyproject.toml here in reqiuirements.txt. On the positive
-side, Binder start-up time could be much smaller (and Binder work at all).
-
-

binder/requirements.txt

@@ -6,3 +6,4 @@ pandas
 pyarrow
 ipython
 pytest
+nbval

book/18-environments.ipynb

@@ -70,7 +70,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Tue Jan  4 16:03:43 CET 2022\r\n"
+      "Wed Jan  5 11:55:11 CET 2022\r\n"
      ]
     }
    ],
@@ -272,7 +272,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "drwxr-xr-x  6 fangohr  staff  192 Jan  4 16:03 \u001b[34mmyvirtualenv/\u001b[m\u001b[m\r\n"
+      "drwxr-xr-x  6 fangohr  staff  192 Jan  5 11:55 \u001b[34mmyvirtualenv/\u001b[m\u001b[m\r\n"
      ]
     }
    ],
@@ -777,20 +777,20 @@
       "  Using cached beautifulsoup4-4.10.0-py3-none-any.whl (97 kB)\n",
       "Collecting requests<3.0.0,>=2.0.0\n",
       "  Using cached requests-2.27.0-py2.py3-none-any.whl (63 kB)\n",
-      "Collecting certifi>=2017.4.17\n",
-      "  Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB)\n",
-      "Collecting urllib3<1.27,>=1.21.1\n",
-      "  Using cached urllib3-1.26.7-py2.py3-none-any.whl (138 kB)\n",
-      "Collecting charset-normalizer~=2.0.0\n",
-      "  Using cached charset_normalizer-2.0.9-py3-none-any.whl (39 kB)\n",
       "Collecting idna<4,>=2.5\n",
       "  Using cached idna-3.3-py3-none-any.whl (61 kB)\n",
+      "Collecting charset-normalizer~=2.0.0\n",
+      "  Using cached charset_normalizer-2.0.10-py3-none-any.whl (39 kB)\n",
+      "Collecting urllib3<1.27,>=1.21.1\n",
+      "  Using cached urllib3-1.26.7-py2.py3-none-any.whl (138 kB)\n",
+      "Collecting certifi>=2017.4.17\n",
+      "  Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB)\n",
       "Collecting soupsieve>1.2\n",
       "  Using cached soupsieve-2.3.1-py3-none-any.whl (37 kB)\n",
       "Using legacy 'setup.py install' for wikipedia, since package 'wheel' is not installed.\n",
       "Installing collected packages: urllib3, soupsieve, idna, charset-normalizer, certifi, requests, beautifulsoup4, wikipedia\n",
       "    Running setup.py install for wikipedia ... \u001b[?25ldone\n",
-      "\u001b[?25hSuccessfully installed beautifulsoup4-4.10.0 certifi-2021.10.8 charset-normalizer-2.0.9 idna-3.3 requests-2.27.0 soupsieve-2.3.1 urllib3-1.26.7 wikipedia-1.4.0\n"
+      "\u001b[?25hSuccessfully installed beautifulsoup4-4.10.0 certifi-2021.10.8 charset-normalizer-2.0.10 idna-3.3 requests-2.27.0 soupsieve-2.3.1 urllib3-1.26.7 wikipedia-1.4.0\n"
      ]
     }
    ],
@@ -834,9 +834,9 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Found existing installation: wikipedia 1.4.0\n",
-      "Uninstalling wikipedia-1.4.0:\n",
-      "  Successfully uninstalled wikipedia-1.4.0\n"
+      "Found existing installation: wikipedia 1.4.0\r\n",
+      "Uninstalling wikipedia-1.4.0:\r\n",
+      "  Successfully uninstalled wikipedia-1.4.0\r\n"
      ]
     }
    ],
@@ -858,7 +858,7 @@
       "------------------ ---------\r\n",
       "beautifulsoup4     4.10.0\r\n",
       "certifi            2021.10.8\r\n",
-      "charset-normalizer 2.0.9\r\n",
+      "charset-normalizer 2.0.10\r\n",
       "idna               3.3\r\n",
       "pip                21.3.1\r\n",
       "requests           2.27.0\r\n",
@@ -1005,9 +1005,9 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Found existing installation: cowsay 4.0\n",
-      "Uninstalling cowsay-4.0:\n",
-      "  Successfully uninstalled cowsay-4.0\n"
+      "Found existing installation: cowsay 4.0\r\n",
+      "Uninstalling cowsay-4.0:\r\n",
+      "  Successfully uninstalled cowsay-4.0\r\n"
      ]
     }
    ],
@@ -1044,8 +1044,8 @@
      "output_type": "stream",
      "text": [
       "Collecting git+https://github.com/VaasuDevanS/cowsay-python.git\n",
-      "  Cloning https://github.com/VaasuDevanS/cowsay-python.git to /private/var/folders/wc/d1lyft3x2jn29b6yffrzh4vw0000gq/T/pip-req-build-3iclfhwr\n",
-      "  Running command git clone --filter=blob:none -q https://github.com/VaasuDevanS/cowsay-python.git /private/var/folders/wc/d1lyft3x2jn29b6yffrzh4vw0000gq/T/pip-req-build-3iclfhwr\n",
+      "  Cloning https://github.com/VaasuDevanS/cowsay-python.git to /private/var/folders/wc/d1lyft3x2jn29b6yffrzh4vw0000gq/T/pip-req-build-7gxyjbt6\n",
+      "  Running command git clone --filter=blob:none -q https://github.com/VaasuDevanS/cowsay-python.git /private/var/folders/wc/d1lyft3x2jn29b6yffrzh4vw0000gq/T/pip-req-build-7gxyjbt6\n",
       "  Resolved https://github.com/VaasuDevanS/cowsay-python.git to commit 767c09425d813b80d67cdebba02ce387ca2eb4e8\n",
       "  Preparing metadata (setup.py) ... \u001b[?25ldone\n",
       "\u001b[?25hUsing legacy 'setup.py install' for cowsay, since package 'wheel' is not installed.\n",
@@ -1120,7 +1120,7 @@
       "remote: Counting objects: 100% (82/82), done.\u001b[K\n",
       "remote: Compressing objects: 100% (40/40), done.\u001b[K\n",
       "remote: Total 170 (delta 41), reused 77 (delta 40), pack-reused 88\u001b[K\n",
-      "Receiving objects: 100% (170/170), 79.19 KiB | 1.15 MiB/s, done.\n",
+      "Receiving objects: 100% (170/170), 79.19 KiB | 772.00 KiB/s, done.\n",
       "Resolving deltas: 100% (72/72), done.\n"
      ]
     }
@@ -1204,7 +1204,7 @@
     }
    ],
    "source": [
-    "!ls myvirtualenv/lib/python3.9/site-packages/cowsay\n"
+    "!ls myvirtualenv/lib/python3.*/site-packages/cowsay\n"
    ]
   },
   {
@@ -1225,9 +1225,9 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Found existing installation: cowsay 4.0\n",
-      "Uninstalling cowsay-4.0:\n",
-      "  Successfully uninstalled cowsay-4.0\n"
+      "Found existing installation: cowsay 4.0\r\n",
+      "Uninstalling cowsay-4.0:\r\n",
+      "  Successfully uninstalled cowsay-4.0\r\n"
      ]
     }
    ],
@@ -1275,12 +1275,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "-rw-r--r--  1 fangohr  staff  28 Jan  4 16:04 myvirtualenv/lib/python3.9/site-packages/cowsay.egg-link\r\n"
+      "-rw-r--r--  1 fangohr  staff  28 Jan  5 11:55 myvirtualenv/lib/python3.9/site-packages/cowsay.egg-link\r\n"
      ]
     }
    ],
    "source": [
-    "!ls -l myvirtualenv/lib/python3.9/site-packages/cowsay*\n"
+    "!ls -l myvirtualenv/lib/python3.*/site-packages/cowsay*\n"
    ]
   },
   {
@@ -1299,7 +1299,7 @@
     }
    ],
    "source": [
-    "!cat myvirtualenv/lib/python3.9/site-packages/cowsay*\n",
+    "!cat myvirtualenv/lib/python3.*/site-packages/cowsay*\n",
     "\n"
    ]
   },
@@ -1331,7 +1331,7 @@
      "text": [
       "beautifulsoup4==4.10.0\r\n",
       "certifi==2021.10.8\r\n",
-      "charset-normalizer==2.0.9\r\n",
+      "charset-normalizer==2.0.10\r\n",
       "-e git+https://github.com/VaasuDevanS/cowsay-python.git@767c09425d813b80d67cdebba02ce387ca2eb4e8#egg=cowsay\r\n",
       "idna==3.3\r\n",
       "requests==2.27.0\r\n",
@@ -1374,7 +1374,7 @@
      "text": [
       "beautifulsoup4==4.10.0\r\n",
       "certifi==2021.10.8\r\n",
-      "charset-normalizer==2.0.9\r\n",
+      "charset-normalizer==2.0.10\r\n",
       "-e git+https://github.com/VaasuDevanS/cowsay-python.git@767c09425d813b80d67cdebba02ce387ca2eb4e8#egg=cowsay\r\n",
       "idna==3.3\r\n",
       "requests==2.27.0\r\n",
@@ -1416,21 +1416,28 @@
      "output_type": "stream",
      "text": [
       "Obtaining cowsay from git+https://github.com/VaasuDevanS/cowsay-python.git@767c09425d813b80d67cdebba02ce387ca2eb4e8#egg=cowsay (from -r requirements.txt (line 4))\n",
-      "  Skipping because already up-to-date.\n",
-      "Requirement already satisfied: beautifulsoup4==4.10.0 in ./myvirtualenv-copy/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (4.10.0)\n",
-      "Requirement already satisfied: certifi==2021.10.8 in ./myvirtualenv-copy/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (2021.10.8)\n",
-      "Requirement already satisfied: charset-normalizer==2.0.9 in ./myvirtualenv-copy/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (2.0.9)\n",
-      "Requirement already satisfied: idna==3.3 in ./myvirtualenv-copy/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (3.3)\n",
-      "Requirement already satisfied: requests==2.27.0 in ./myvirtualenv-copy/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (2.27.0)\n",
-      "Requirement already satisfied: soupsieve==2.3.1 in ./myvirtualenv-copy/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (2.3.1)\n",
-      "Requirement already satisfied: urllib3==1.26.7 in ./myvirtualenv-copy/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (1.26.7)\n",
-      "Installing collected packages: cowsay\n",
-      "  Attempting uninstall: cowsay\n",
-      "    Found existing installation: cowsay 4.0\n",
-      "    Uninstalling cowsay-4.0:\n",
-      "      Successfully uninstalled cowsay-4.0\n",
+      "  Cloning https://github.com/VaasuDevanS/cowsay-python.git (to revision 767c09425d813b80d67cdebba02ce387ca2eb4e8) to ./myvirtualenv-copy/src/cowsay\n",
+      "  Running command git clone -q https://github.com/VaasuDevanS/cowsay-python.git /Users/fangohr/git/introduction-to-python-for-computational-science-and-engineering/book/myvirtualenv-copy/src/cowsay\n",
+      "  Running command git rev-parse -q --verify 'sha^767c09425d813b80d67cdebba02ce387ca2eb4e8'\n",
+      "  Running command git fetch -q https://github.com/VaasuDevanS/cowsay-python.git 767c09425d813b80d67cdebba02ce387ca2eb4e8\n",
+      "  Resolved https://github.com/VaasuDevanS/cowsay-python.git to commit 767c09425d813b80d67cdebba02ce387ca2eb4e8\n",
+      "Collecting beautifulsoup4==4.10.0\n",
+      "  Using cached beautifulsoup4-4.10.0-py3-none-any.whl (97 kB)\n",
+      "Collecting certifi==2021.10.8\n",
+      "  Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB)\n",
+      "Collecting charset-normalizer==2.0.10\n",
+      "  Using cached charset_normalizer-2.0.10-py3-none-any.whl (39 kB)\n",
+      "Collecting idna==3.3\n",
+      "  Using cached idna-3.3-py3-none-any.whl (61 kB)\n",
+      "Collecting requests==2.27.0\n",
+      "  Using cached requests-2.27.0-py2.py3-none-any.whl (63 kB)\n",
+      "Collecting soupsieve==2.3.1\n",
+      "  Using cached soupsieve-2.3.1-py3-none-any.whl (37 kB)\n",
+      "Collecting urllib3==1.26.7\n",
+      "  Using cached urllib3-1.26.7-py2.py3-none-any.whl (138 kB)\n",
+      "Installing collected packages: urllib3, soupsieve, idna, charset-normalizer, certifi, requests, cowsay, beautifulsoup4\n",
       "  Running setup.py develop for cowsay\n",
-      "Successfully installed cowsay-4.0\n",
+      "Successfully installed beautifulsoup4-4.10.0 certifi-2021.10.8 charset-normalizer-2.0.10 cowsay-4.0 idna-3.3 requests-2.27.0 soupsieve-2.3.1 urllib3-1.26.7\n",
       "\u001b[33mWARNING: You are using pip version 21.2.3; however, version 21.3.1 is available.\n",
       "You should consider upgrading via the '/Users/fangohr/git/introduction-to-python-for-computational-science-and-engineering/book/myvirtualenv-copy/bin/python -m pip install --upgrade pip' command.\u001b[0m\n"
      ]
@@ -1673,4 +1680,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}