update dockerfile base (#421)

* update dockerfile base
* also using default models JsonField and setting default autofield
* pin django 4.2

Signed-off-by: vsoch <[email protected]>

.all-contributorsrc

@@ -228,4 +228,4 @@
         }
     ],
     "contributorsPerLine": 7
-}
+}

.circleci/config.yml

@@ -4,7 +4,7 @@
 # defined here or within the CircleCI settings. The following environment
 # variables are acceptable here or in these settings (for sensitive information)
 #
-# CONTAINER_NAME if not set, will use Github repo and organization name 
+# CONTAINER_NAME if not set, will use Github repo and organization name
 # DOCKER_USER
 # DOCKER_EMAIL
 # Dockerfile optional, if the path is different than the Dockerfile in $PWD
@@ -30,7 +30,7 @@ install: &install
 
 sourceenv: &sourceenv
     name: Source environment variables from the BASH_ENV
-    command: source $BASH_ENV 
+    command: source $BASH_ENV
 
 
 # Docker
@@ -67,7 +67,7 @@ dockerenv: &dockerenv
 dockerload: &dockerload
     name: Load Docker container Image
     no_output_timeout: 30m
-    command: | 
+    command: |
       echo "Working directory is ${PWD}"
       docker info
       set +o pipefail
@@ -128,7 +128,7 @@ dockernginx: &dockernginx
     name: Build nginx custom container
     command: |
       source ${BASH_ENV}
-      echo "Building ${CONTAINER_NAME}_nginx:${DOCKER_TAG}"      
+      echo "Building ${CONTAINER_NAME}_nginx:${DOCKER_TAG}"
       cd ${REPO_NAME}/nginx && \
       ls && \
       docker build -f ${DOCKERFILE} -t ${CONTAINER_NAME}_nginx:${DOCKER_TAG} .
@@ -196,7 +196,7 @@ workflows:
       - build:
           filters:
             branches:
-              ignore: 
+              ignore:
                 - gh-pages
                 - /docs?/.*/
                 - contributors/*
@@ -208,7 +208,7 @@ workflows:
             - build
           filters:
             branches:
-              ignore: 
+              ignore:
                 - gh-pages
                 - /docs?/.*/
                 - contributors/*

.github/CONTRIBUTING.md

@@ -25,8 +25,8 @@ all your interactions with the project members and users.
 4. The project's default copyright and header have been included in any new
    source files.
 5. All (major) changes to Singularity Registry must be documented in
-   [docs](docs). If your PR changes a core functionality, please 
-   include clear description of the changes in your PR so that the docs 
+   [docs](docs). If your PR changes a core functionality, please
+   include clear description of the changes in your PR so that the docs
    can be updated, or better, submit another PR to update the docs directly.
 6. If necessary, update the README.md.
 7. The pull request will be reviewed by others, and the final merge must be
@@ -98,7 +98,7 @@ an incident. Further details of specific enforcement policies may be posted
 separately.
 
 Project maintainers, contributors and users who do not follow or enforce the
-Code of Conduct in good faith may face temporary or permanent repercussions 
+Code of Conduct in good faith may face temporary or permanent repercussions
 with their involvement in the project as determined by the project's leader(s).
 
 ## Attribution

.github/ISSUE_TEMPLATE/question.md

@@ -3,5 +3,3 @@ name: Question
 about: What's on your mind?
 
 ---
-
-

.github/ISSUE_TEMPLATE/request-for-documentation-or-tutorial.md

@@ -3,5 +3,3 @@ name: Request for Documentation or Tutorial
 about: request improvements or changes to docs or a tutorial
 
 ---
-
-

.github/dev-requirements.txt

@@ -0,0 +1,4 @@
+pre-commit
+black
+isort
+flake8

.github/workflows/main.yml

@@ -14,15 +14,16 @@ jobs:
       - uses: actions/checkout@v1
 
       - name: Check for typos in docs
-        uses: crate-ci/typos@592b36d23c62cb378f6097a292bc902ee73f93ef # version 1.0.4
-        with: 
-          files: ./docs ./README.md
+        uses: crate-ci/typos@7ad296c72fa8265059cc03d1eda562fbdfcd6df2 # v1.9.0
+        with:
+           files: ./docs/_docs ./docs/_posts ./README.md
 
       - name: Setup black linter
         run: conda create --quiet --name black black
 
-      - name: Lint python code
+      - name: Lint and format Python code
         run: |
           export PATH="/usr/share/miniconda/bin:$PATH"
           source activate black
-          black --check shub
+          pip install -r .github/dev-requirements.txt
+          pre-commit run --all-files

.github/workflows/update-contributors.yml

@@ -13,12 +13,12 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v2
       - name: Tributors Update
-      
+
         # Important! Update to release https://github.com/con/tributors
         uses: con/[email protected]
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:        
+        with:
 
           # Single text list (space separated) of parsers, leave unset to auto-detect
           parsers: unset

.gitignore

@@ -11,6 +11,7 @@ Gemfile.lock
 sregistry
 _site
 minio-images
+env
 
 # Other #
 #########

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+exclude: "(.all-contributorsrc|static)"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: mixed-line-ending
+
+  - repo: local
+    hooks:
+      - id: black
+        name: black
+        language: python
+        types: [python]
+        entry: black
+
+      - id: isort
+        name: isort
+        args: [--filter-files]
+        language: python
+        types: [python]
+        entry: isort
+
+      - id: flake8
+        name: flake8
+        language: python
+        types: [python]
+        entry: flake8

.tributors

@@ -117,4 +117,4 @@
         "affiliation": "Fraunhofer-Institut für Zelltherapie und Immunologie",
         "blog": "https://github.com/SethosII"
     }
-}
+}

CHANGELOG.md

@@ -1,8 +1,8 @@
 # CHANGELOG
 
-This is a manually generated log to track changes to the repository for each release. 
-Each section should include general headers such as **Implemented enhancements** 
-and **Merged pull requests**. All closed issued and bug fixes should be 
+This is a manually generated log to track changes to the repository for each release.
+Each section should include general headers such as **Implemented enhancements**
+and **Merged pull requests**. All closed issued and bug fixes should be
 represented by the pull requests that fixed them. Critical items to know are:
 
  - renamed commands
@@ -12,11 +12,12 @@ represented by the pull requests that fixed them. Critical items to know are:
 
 
 ## [master](https://github.com/singularityhub/sregistry/tree/master) (master)
+ - update to use Django 4.2 (2.1.0)
  - consolidate config into one file with environment (2.0.0)
    - This is an API breaking change, as the settings are completely refactored
  - update python base to 3.9, minio server to use new credentials (1.1.4)
    - docker-compose updated to use docker compose
- - add: auto set "verify" attribute of s3 and s3_external obj in minio.py for SSL use (1.1.39) 
+ - add: auto set "verify" attribute of s3 and s3_external obj in minio.py for SSL use (1.1.39)
  - fix issues with psycopg2-binary and saml auth (1.1.38)
    - Pin psycopg2-binary 2.8.6 to deal with UTC errors
    - change formatting of the login URL to fix saml auth

Dockerfile

@@ -1,7 +1,7 @@
 FROM python:3.9
 ENV PYTHONUNBUFFERED 1
-ENV DEBIAN_FRONTEND noninteractive
-ENV MESSAGELEVEL QUIET
+ENV DEBIAN_FRONTEND=noninteractive
+ENV MESSAGELEVEL=QUIET
 
 ARG ENABLE_LDAP=false
 ARG ENABLE_PAM=false

README.md

@@ -55,13 +55,13 @@
 
 ## What is Singularity Registry
 
-Singularity Registry Server is a server to provide management and storage of 
-Singularity images for an institution or user to deploy locally. 
-It does not manage building but serves endpoints to obtain and save containers. 
+Singularity Registry Server is a server to provide management and storage of
+Singularity images for an institution or user to deploy locally.
+It does not manage building but serves endpoints to obtain and save containers.
 
 ## Images Included
 
-Singularity Registry consists of several Docker images, and they are integrated 
+Singularity Registry consists of several Docker images, and they are integrated
 to work together using [docker-compose.yml](docker-compose.yml).
 
 The images are the following:

VERSION

@@ -1 +1 @@
-2.0.0
+2.1.0

docker-compose.yml

@@ -16,7 +16,7 @@ services:
       - ./static:/var/www/static
       - ./images:/var/www/images
       # uncomment for PAM auth
-      #- /etc/passwd:/etc/passwd 
+      #- /etc/passwd:/etc/passwd
       #- /etc/shadow:/etc/shadow
     links:
       - minio
@@ -73,11 +73,12 @@ services:
       - db
 
   minio:
-    image: minio/minio
+    # https://min.io/docs/minio/linux/operations/install-deploy-manage/migrate-fs-gateway.html
+    image: minio/minio:RELEASE.2022-08-02T23-59-16Z
     volumes:
       - ./minio-images:/images
     env_file:
      - ./.minio-env
     ports:
-     - "9000:9000"  
+     - "9000:9000"
     command: ["server", "images"]

docs/CHANGELOG.md

@@ -1,8 +1,8 @@
 # Changelog
 
-This is a manually generated log to track changes to the repository for each release. 
-Each section should include general headers such as **Implemented enhancements** 
-and **Merged pull requests**. All closed issued and bug fixes should be 
+This is a manually generated log to track changes to the repository for each release.
+Each section should include general headers such as **Implemented enhancements**
+and **Merged pull requests**. All closed issued and bug fixes should be
 represented by the pull requests that fixed them.
 Critical items to know are:
 

docs/README.md

@@ -24,7 +24,7 @@ cd docs
 ### 2. Customize
 
 To edit configuration values, customize the [_config.yml](_config.yml).
-To add pages, write them into the [pages](pages) folder. 
+To add pages, write them into the [pages](pages) folder.
 You define urls based on the `permalink` attribute in your pages,
 and then add them to the navigation by adding to the content of [_data/toc.myl](_data/toc.yml).
 

docs/_docs/accounts/README.md

@@ -9,7 +9,7 @@ permalink: docs/accounts/
 
 Singularity Registry server creates user accounts by way of login with OAuth2, and
 then interaction with the API via user specific tokens. These sections describe
-how to generate accounts, teams, as well as robot users for interacting with 
+how to generate accounts, teams, as well as robot users for interacting with
 continuous integration.
 
  - [credentials](credentials): overview of basic accounts and credentials

docs/_docs/accounts/credentials.md

@@ -29,7 +29,7 @@ docker exec $NAME python /code/manage.py add_superuser --username vsoch
 docker exec $NAME python /code/manage.py add_admin --username vsoch
 ```
 
-You will want to go to [http://127.0.0.1/token](http://127.0.0.1/token) and use the contents of the json object to define the necessary environment variabes. 
+You will want to go to [http://127.0.0.1/token](http://127.0.0.1/token) and use the contents of the json object to define the necessary environment variables.
 
 {% include alert.html title="Important!" content="You must be a superuser <strong>and</strong> admin to build images." %}
 

docs/_docs/accounts/robots.md

@@ -39,7 +39,7 @@ collection.save()
 ```
 
 As an alternative, if you intend to add this robot user to more than one collection,
-you can create a [Team]({{ site.url }}{{ site.baseurl }}/docs/setup/teams) in the interface, 
+you can create a [Team]({{ site.url }}{{ site.baseurl }}/docs/setup/teams) in the interface,
 add the robot user to it also via the console:
 
 ```python

docs/_docs/client.md

@@ -8,10 +8,10 @@ toc: false
 
 ## Singularity Pull
 
-Singularity Registry Server implements a basic version of the Sylabs Library API, 
-meaning that you can pull a container with Singularity directly. 
+Singularity Registry Server implements a basic version of the Sylabs Library API,
+meaning that you can pull a container with Singularity directly.
 
-**Important** you must be using Singularity 3.3.0 or greater for this to work! 
+**Important** you must be using Singularity 3.3.0 or greater for this to work!
 If not, you should use [Singularity Registry Client](#singularity-registry-client)
  (which also has examples below of using the `shub://` endpoint with singularity).
 
@@ -90,7 +90,7 @@ And then provide it (via copy paste) to the Singularity client to create a remot
 $ singularity remote login DinosaurCloud
 Generate an access token at http://127.0.0.1/auth/tokens, and paste it here.
 Token entered will be hidden for security.
-Access Token: 
+Access Token:
 INFO:    Access Token Verified!
 INFO:    Token stored in /home/vanessa/.singularity/remote.yaml
 ```
@@ -101,7 +101,7 @@ If you paste a token that isn't valid, you'll get a different message
 $ singularity remote login DinosaurCloud
 INFO:    Authenticating with remote: DinosaurCloud
 Generate an API Key at https://127.0.0.1/auth/tokens, and paste here:
-API Key: 
+API Key:
 FATAL:   while verifying token: error response from server: Invalid Token
 ```
 
@@ -138,7 +138,7 @@ $ singularity remote use DinosaurCloud
 Now that we have a token, let's try a push! For security purposes, the collection
 should already exist, and be owned by you. Collaborators are not allowed to push.
 
-```bash 
+```bash
                                          # library://user/collection/container[:tag]
 $ singularity push -U busybox_latest.sif library://vsoch/dinosaur-collection/another:latest
 ```
@@ -245,7 +245,7 @@ Not shown in the demo above is the pull command, but it does the same thing as t
 
 ```bash
 sregistry pull banana/pudding:milkshake
-Progress |===================================| 100.0% 
+Progress |===================================| 100.0%
 Success! banana-pudding-milkshake.img
 ```
 
@@ -342,7 +342,7 @@ sregistry labels --key maintainer --value vanessasaur
 
 # Curl
 
-Like with the Sylabs Library API, it is possible to interact with Singularity Registry Server 
+Like with the Sylabs Library API, it is possible to interact with Singularity Registry Server
 using Curl. You can browse the API schema via the `/api` path of your server.
 
 ## Authentication
@@ -400,7 +400,7 @@ a POST request to the endpoint `/v1/collections` and this json payload:
 Here is an example with our user id of 1:
 
 ```bash
-$ curl -X POST -H 'Authorization: Bearer <token>' -H "Content-Type: application/json" --data '{"entity": 1, "name": "dinosaurs"}' http://127.0.0.1/v1/collections 
+$ curl -X POST -H 'Authorization: Bearer <token>' -H "Content-Type: application/json" --data '{"entity": 1, "name": "dinosaurs"}' http://127.0.0.1/v1/collections
 ```
 
 You can then see the response that the collection was created, and it will appear in the interface:

docs/_docs/deploy/ansible.md

@@ -45,5 +45,5 @@ Once you have completed all the configuration of the role in your recipe, it is
 sudo ansible-playbook sregistry.yml
 ```
 
-Want to learn more? Check out the [official documentation](https://github.com/grycap/ansible-role-singularity-registry) 
+Want to learn more? Check out the [official documentation](https://github.com/grycap/ansible-role-singularity-registry)
 for the entire story.