Merge branch 'FAIRmat-NFDI:main' into install-apt-get

.github/workflows/initialize.yml

@@ -25,11 +25,13 @@ jobs:
       # Replaces the template repository name in the README with the new one
       - name: Update README
         run: |
-          sed -i "s|GITHUB_REPOSITORY_OWNER|${{ github.repository_owner }}|g" template_README.md
-          sed -i "s|GITHUB_REPOSITORY_NAME|${{ github.event.repository.name }}|g" template_README.md
-          sed -i "s|GITHUB_REPOSITORY|${{ github.repository }}|g" template_README.md
-          sed -i "s|GITHUB_REPOSITORY_NAME|${{ github.event.repository.name }}|g" template_README.md
-          mv template_README.md README.md
+          sed -i "/# NOMAD Oasis Distribution/,/button on the right./d" README.md
+          sed -i "s|FAIRmat-NFDI/nomad-distribution-template|${{ github.repository }}|g" README.md
+          sed -i "s|FAIRmat-NFDI|${{ github.repository_owner }}|g" README.md
+          sed -i "s|nomad-distribution-template|${{ github.event.repository.name }}|g" README.md
+          sed -i "s|template https://github.com/${{ github.repository }}|template https://github.com/FAIRmat-NFDI/nomad-distribution-template|g" README.md
+          sed -i "s|${{ github.repository }}/releases/latest|FAIRmat-NFDI/nomad-distribution-template/releases/latest|g" README.md
+          sed -i "s|@ git+https://github.com/${{ github.repository_owner }}|@ git+https://github.com/FAIRmat-NFDI|g" README.md
 
       # Replaces the template repository name in the docker config file with the new one
       - name: Update docker-compose.yaml

README.md

@@ -1,14 +1,211 @@
 ![docker image](https://github.com/FAIRmat-NFDI/nomad-distribution-template/actions/workflows/docker-publish.yml/badge.svg)
 
+# NOMAD Oasis Distribution *Template*
+This repository is a template for creating your own custom NOMAD Oasis distribution image.
+Click [here](https://github.com/new?template_name=nomad-distribution-template&template_owner=FAIRmat-NFDI)
+to use this template, or click the `Use this template` button in the upper right corner of
+the main GitHub page for this template.
+
 > [!IMPORTANT] 
 > The templated repository will run a GitHub action on creation which might take a few minutes.
 > After the workflow finishes you should refresh the page and this message should disappear.
 > If this message persists you might need to trigger the workflow manually by navigating to the
 > "Actions" tab at the top, clicking "Template Repository Initialization" on the left side,
 > and triggering it by clicking "Run workflow" under the "Run workflow" button on the right.
 
-# NOMAD Oasis Distribution *Template*
-This repository is a template for creating your own custom NOMAD Oasis distribution image.
-Click [here](https://github.com/new?template_name=nomad-distribution-template&template_owner=FAIRmat-NFDI)
-to use this template, or click the `Use this template` button in the upper right corner of
-the main GitHub page for this template.
+# FAIRmat-NFDI's NOMAD Oasis Distribution
+
+This is the NOMAD Oasis distribution of FAIRmat-NFDI.
+Below are instructions for how to [deploy this distribution](#deploying-the-distribution)
+and how to customize it through [adding plugins](#adding-a-plugin).
+
+> [!IMPORTANT]
+> Depending on the settings of the owner of this repository, the distributed image might
+> be private and require authentication to pull.
+> If you want to keep the image private you need to configure and use a personal access
+> token (PAT) according to the instructions in the GitHub docs [here](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry#authenticating-with-a-personal-access-token-classic).
+> If you want to make the image public (recommended), you should make sure that your
+> organization settings allow public packages and make this package public after building it.
+> You can read more about this in the GitHub docs [here](https://docs.github.com/en/packages/learn-github-packages/configuring-a-packages-access-control-and-visibility).
+
+> [!TIP]
+> In order for others to find and learn from your distribution we in FAIRmat would
+> greatly appreciate it if you would add the topic `nomad-distribution` by clicking the
+> ⚙️ next to "About" on the main GitHub page for this repository.
+
+In this README you will find instructions for:
+1. [Deploying the distribution](#deploying-the-distribution)
+2. [Adding a plugin](#adding-a-plugin)
+3. [Updating the distribution from the template](#updating-the-distribution-from-the-template)
+4. [Solving common issues](#faqtrouble-shooting)
+
+## Deploying the distribution
+
+Below are instructions for how to deploy this NOMAD Oasis distribution
+[for a new Oasis](#for-a-new-oasis) and [for an existing Oasis](#for-an-existing-oasis)
+
+### For a new Oasis
+
+1. Make sure you have [docker](https://docs.docker.com/engine/install/) installed.
+   Docker nowadays comes with `docker compose` built in. Prior, you needed to
+   install the stand-alone [docker-compose](https://docs.docker.com/compose/install/).
+
+2. Clone the repository or download the repository as a zip file.
+
+    ```sh
+    git clone https://github.com/FAIRmat-NFDI/nomad-distribution-template.git
+    cd nomad-distribution-template
+    ```
+
+    or
+
+    ```sh
+    curl-L -o nomad-distribution-template.zip "https://github.com/FAIRmat-NFDI/nomad-distribution-template/archive/main.zip"
+    unzip nomad-distribution-template.zip
+    cd nomad-distribution-template
+    ```
+
+3. _On Linux only,_ recursively change the owner of the `.volumes` directory to the nomad user (1000)
+
+    ```sh
+    sudo chown -R 1000 .volumes
+    ```
+
+4. Pull the images specified in the `docker-compose.yaml`
+
+    Note that the image needs to be public or you need to provide a PAT (see "Important" note above).
+
+    ```sh
+    docker compose pull
+    ```
+
+5. And run it with docker compose in detached (--detach or -d) mode
+
+    ```sh
+    docker compose up -d
+    ```
+
+6. Optionally you can now test that NOMAD is running with
+
+    ```
+    curl localhost/nomad-oasis/alive
+    ```
+
+7. Finally, open [http://localhost/nomad-oasis](http://localhost/nomad-oasis) in your browser to start using your new NOMAD Oasis.
+
+    Whenever you update your image you need to shut down NOMAD using
+
+    ```sh
+    docker compose down
+    ```
+
+    and then repeat steps 4. and 5. above.
+
+#### NOMAD Remote Tools Hub (NORTH)
+
+To run NORTH (the NOMAD Remote Tools Hub), the `hub` container needs to run docker and
+the container has to be run under the docker group. You need to replace the default group
+id `991` in the `docker-compose.yaml`'s `hub` section with your systems docker group id.
+Run `id` if you are a docker user, or `getent group | grep docker` to find your
+systems docker gid. The user id 1000 is used as the nomad user inside all containers.
+
+You can find more details on setting up and maintaining an Oasis in the NOMAD docs here:
+[nomad-lab.eu/prod/v1/docs/oasis/install.html](https://nomad-lab.eu/prod/v1/docs/oasis/install.html)
+
+### For an existing Oasis
+
+If you already have an Oasis running you only need to change the image being pulled in
+your `docker-compose.yaml` with `ghcr.io/FAIRmat-NFDI/nomad-distribution-template:main` for the services
+`worker`, `app`, `north`, and `logtransfer`.
+
+If you want to use the `nomad.yaml` from this repository you also need to comment out
+the inclusion of the `nomad.yaml` under the volumes key of those services in the
+`docker-compose.yaml`.
+
+```yaml
+volumes:
+  # - ./configs/nomad.yaml:/app/nomad.yaml
+```
+
+To run the new image you can follow steps 5. and 6. [above](#for-a-new-oasis).
+
+## Adding a plugin
+
+To add a new plugin to the docker image you should add it to the plugins table in the `pyproject.toml` file.
+
+Here you can put either plugins distributed to PyPI, e.g.
+
+```toml
+[project.optional-dependencies]
+plugins = [
+  "nomad-material-processing>=1.0.0",
+]
+```
+
+or plugins in a git repository with either the commit hash
+
+```toml
+[project.optional-dependencies]
+plugins = [
+  "nomad-measurements @ git+https://github.com/FAIRmat-NFDI/nomad-measurements.git@71b7e8c9bb376ce9e8610aba9a20be0b5bce6775",
+]
+```
+
+or with a tag
+
+```toml
+[project.optional-dependencies]
+plugins = [
+  "nomad-measurements @ git+https://github.com/FAIRmat-NFDI/[email protected]"
+]
+```
+
+To add a plugin in a subdirectory of a git repository you can use the `subdirectory` option, e.g.
+
+```toml
+[project.optional-dependencies]
+plugins = [
+  "ikz_pld_plugin @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@30fc90843428d1b36a1d222874803abae8b1cb42#subdirectory=PVD/PLD/jeremy_ikz/ikz_pld_plugin"
+]
+```
+
+Once the changes have been committed to the main branch, the new image will automatically
+be generated.
+
+## Updating the distribution from the template
+
+In order to update an existing distribution with any potential changes in the template you can add a new `git remote` for the template and merge with that one while allowing for unrelated histories:
+
+```
+git remote add template https://github.com/FAIRmat-NFDI/nomad-distribution-template
+git fetch template
+git merge template/main --allow-unrelated-histories
+```
+
+Most likely this will result in some merge conflicts which will need to be resolved. At the very least the `Dockerfile` and GitHub workflows should be taken from "theirs":
+
+```
+git checkout --theirs Dockerfile
+git checkout --theirs .github/workflows/docker-publish.yml
+```
+
+For detailed instructions on how to resolve the merge conflicts between different version we refer you to the latest template release [notes](https://github.com/FAIRmat-NFDI/nomad-distribution-template/releases/latest)
+
+Once the merge conflicts are resolved you should add the changes and commit them
+
+```
+git add -A
+git commit -m "Updated to new distribution version"
+```
+
+Ideally all workflows should be triggered automatically but you might need to run the initialization one manually by navigating to the "Actions" tab at the top, clicking "Template Repository Initialization" on the left side, and triggering it by clicking "Run workflow" under the "Run workflow" button on the right.
+
+## FAQ/Trouble shooting
+
+_I get an_ `Error response from daemon: Head "https://ghcr.io/v2/FAIRmat-NFDI/nomad-distribution-template/manifests/main": unauthorized`
+_when trying to pull my docker image._
+
+Most likely you have not made the package public or provided a personal access token (PAT).
+You can read how to make your package public in the GitHub docs [here](https://docs.github.com/en/packages/learn-github-packages/configuring-a-packages-access-control-and-visibility)
+or how to configure a PAT (if you want to keep the distribution private) in the GitHub
+docs [here](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry#authenticating-with-a-personal-access-token-classic).

pyproject.toml

@@ -47,6 +47,7 @@ extra-index-url = [
   "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple",
 ]
 constraint-dependencies = ["hyperspy>=1.7.6"]
+prerelease = "disallow"
 
 [tool.setuptools.packages.find]
 exclude = ["gui*", "docs*", "config*"]