initial setup

.github/pull_request_template.md

@@ -10,9 +10,9 @@ Changes proposed in this pull request:
 ## Before submitting
 
 <!-- Please complete this checklist BEFORE submitting your PR to speed along the review process. -->
-- [ ] I've read and followed all steps in the [Making a pull request](https://github.com/precimed/container_template/blob/main/CONTRIBUTING.md#making-a-pull-request)
+- [ ] I've read and followed all steps in the [Making a pull request](https://github.com/comorment/mtag_container/blob/main/CONTRIBUTING.md#making-a-pull-request)
     section of the `CONTRIBUTING` docs.
 - [ ] I've updated or added any relevant docstrings following the syntax described in the
-    [Writing docstrings](https://github.com/precimed/container_template/blob/main/CONTRIBUTING.md#writing-docstrings) section of the `CONTRIBUTING` docs.
+    [Writing docstrings](https://github.com/comorment/mtag_container/blob/main/CONTRIBUTING.md#writing-docstrings) section of the `CONTRIBUTING` docs.
 - [ ] If this PR fixes a bug, I've added a test that will fail without my fix.
 - [ ] If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

.github/workflows/container_build.yml

@@ -10,8 +10,8 @@ on:
     tags:
       - "v*.*.*"
 env:
-  TEST_TAG: ghcr.io/precimed/container_template:test
-  # LATEST_TAG: ghcr.io/precimed/container_template:latest
+  TEST_TAG: ghcr.io/comorment/mtag_container:test
+  # LATEST_TAG: ghcr.io/comorment/mtag_container:latest
 
 jobs:
   docker:
@@ -25,7 +25,7 @@ jobs:
         with:
           # list of Docker images to use as base name for tags
           images: |
-            ghcr.io/${{ github.repository_owner }}/container_template            
+            ghcr.io/${{ github.repository_owner }}/mtag_container            
           # generate Docker tags based on the following events/attributes
           tags: |
             type=schedule
@@ -55,7 +55,7 @@ jobs:
           load: true
           tags: ${{ env.TEST_TAG }}
           file:
-            ./dockerfiles/container_template/Dockerfile
+            ./dockerfiles/mtag_container/Dockerfile
 
       - name: Run unit tests
         run: |
@@ -69,5 +69,5 @@ jobs:
           load: True
           tags: ${{ steps.meta.outputs.tags }}
           file:
-            ./dockerfiles/container_template/Dockerfile
+            ./dockerfiles/mtag_container/Dockerfile
           platforms: linux/amd64

.github/workflows/container_build_push.yml

@@ -6,7 +6,7 @@ on:
       - "v*.*.*"
 
 env:
-  TEST_TAG: ghcr.io/precimed/container_template:test
+  TEST_TAG: ghcr.io/comorment/mtag_container:test
 
 jobs:
   docker:
@@ -20,7 +20,7 @@ jobs:
         with:
           # list of Docker images to use as base name for tags
           images: |
-            ghcr.io/${{ github.repository_owner }}/container_template            
+            ghcr.io/${{ github.repository_owner }}/mtag_container            
           # generate Docker tags based on the following events/attributes
           tags: |
             type=schedule
@@ -50,7 +50,7 @@ jobs:
           load: true
           tags: ${{ env.TEST_TAG }}
           file:
-            ./dockerfiles/container_template/Dockerfile
+            ./dockerfiles/mtag_container/Dockerfile
       - name: Test
         run: |
           docker run --rm -v ${{ github.workspace }}:/home ${{ env.TEST_TAG }} py.test -v tests
@@ -63,7 +63,7 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           file:
-            ./dockerfiles/container_template/Dockerfile
+            ./dockerfiles/mtag_container/Dockerfile
           platforms: linux/amd64
 
   build-apptainer-container:
@@ -81,7 +81,7 @@ jobs:
         uses: docker/metadata-action@v5
         with:
           images: |
-            ghcr.io/${{ github.repository_owner }}/container_template            
+            ghcr.io/${{ github.repository_owner }}/mtag_container            
           tags: |
             type=semver,pattern={{version}}
             type=ref,event=branch
@@ -94,10 +94,10 @@ jobs:
           IFS= read -r first_tag <<EOF
           $tags
           EOF
-          push_tags="$(printf $csv_tags | sed -e "s/container_template/container_template_sif/g")"
+          push_tags="$(printf $csv_tags | sed -e "s/mtag_container/mtag_container_sif/g")"
           echo ${{ secrets.GITHUB_TOKEN }} | oras login --username ${{ github.repository_owner }} --password-stdin ghcr.io
           docker pull kaczmarj/apptainer:latest
-          docker run --rm --privileged -v $(pwd):/work kaczmarj/apptainer build container_template.sif docker://"$first_tag"
-          oras push "$push_tags" container_template.sif
-          rm container_template.sif
+          docker run --rm --privileged -v $(pwd):/work kaczmarj/apptainer build mtag_container.sif docker://"$first_tag"
+          oras push "$push_tags" mtag_container.sif
+          rm mtag_container.sif
         shell: sh

CONTRIBUTING.md

@@ -6,10 +6,10 @@ Thanks for considering contributing! Please read this document to learn the vari
 
 ### Did you find a bug?
 
-First, do [a quick search](https://github.com/precimed/container_template/issues) to see whether your issue has already been reported.
+First, do [a quick search](https://github.com/comorment/mtag_container/issues) to see whether your issue has already been reported.
 If your issue has already been reported, please comment on the existing issue.
 
-Otherwise, open [a new GitHub issue](https://github.com/precimed/container_template/issues).  Be sure to include a clear title
+Otherwise, open [a new GitHub issue](https://github.com/comorment/mtag_container/issues).  Be sure to include a clear title
 and description.  The description should include as much relevant information as possible.  The description should
 explain how to reproduce the erroneous behavior as well as the behavior you expect to see.  Ideally you would include a
 code sample or an executable test case demonstrating the expected behavior.
@@ -21,7 +21,7 @@ We use GitHub issues to track feature requests. Before you create a feature requ
 * Make sure you have a clear idea of the enhancement you would like. If you have a vague idea, consider discussing
 it first on a GitHub issue.
 * Check the documentation to make sure your feature does not already exist.
-* Do [a quick search](https://github.com/precimed/container_template/issues) to see whether your feature has already been suggested.
+* Do [a quick search](https://github.com/comorment/mtag_container/issues) to see whether your feature has already been suggested.
 
 When creating your request, please:
 
@@ -41,37 +41,37 @@ When you're ready to contribute code to address an open issue, please follow the
 
     Then clone your fork locally with
 
-        git clone https://github.com/USERNAME/container_template.git
+        git clone https://github.com/USERNAME/mtag_container.git
 
     or
 
-        git clone [email protected]:USERNAME/container_template.git
+        git clone [email protected]:USERNAME/mtag_container.git
 
-    At this point the local clone of your fork only knows that it came from *your* repo, github.com/USERNAME/container_template.git, but doesn't know anything the *main* repo, [https://github.com/precimed/container_template.git](https://github.com/precimed/container_template). You can see this by running
+    At this point the local clone of your fork only knows that it came from *your* repo, github.com/USERNAME/mtag_container.git, but doesn't know anything the *main* repo, [https://github.com/comorment/mtag_container.git](https://github.com/comorment/mtag_container). You can see this by running
 
         git remote -v
 
     which will output something like this:
 
-        origin https://github.com/USERNAME/container_template.git (fetch)
-        origin https://github.com/USERNAME/container_template.git (push)
+        origin https://github.com/USERNAME/mtag_container.git (fetch)
+        origin https://github.com/USERNAME/mtag_container.git (push)
 
-    This means that your local clone can only track changes from your fork, but not from the main repo, and so you won't be able to keep your fork up-to-date with the main repo over time. Therefore you'll need to add another "remote" to your clone that points to [https://github.com/precimed/container_template.git](https://github.com/precimed/container_template). To do this, run the following:
+    This means that your local clone can only track changes from your fork, but not from the main repo, and so you won't be able to keep your fork up-to-date with the main repo over time. Therefore you'll need to add another "remote" to your clone that points to [https://github.com/comorment/mtag_container.git](https://github.com/comorment/mtag_container). To do this, run the following:
 
-        git remote add upstream https://github.com/precimed/container_template.git
+        git remote add upstream https://github.com/comorment/mtag_container.git
 
     Now if you do `git remote -v` again, you'll see
 
-        origin https://github.com/USERNAME/container_template.git (fetch)
-        origin https://github.com/USERNAME/container_template.git (push)
-        upstream https://github.com/precimed/container_template.git (fetch)
-        upstream https://github.com/precimed/container_template.git (push)
+        origin https://github.com/USERNAME/mtag_container.git (fetch)
+        origin https://github.com/USERNAME/mtag_container.git (push)
+        upstream https://github.com/comorment/mtag_container.git (fetch)
+        upstream https://github.com/comorment/mtag_container.git (push)
 
 2. **Ensure your fork is up-to-date**
 
     <details><summary>Expand details 👇</summary><br/>
 
-    Once you've added an "upstream" remote pointing to [https://github.com/precimed/container_template.git](https://github.com/precimed/container_template), keeping your fork up-to-date is easy:
+    Once you've added an "upstream" remote pointing to [https://github.com/comorment/mtag_container.git](https://github.com/comorment/mtag_container), keeping your fork up-to-date is easy:
 
         git checkout main  # if not already on main
         git pull --rebase upstream main
@@ -97,12 +97,12 @@ When you're ready to contribute code to address an open issue, please follow the
 
     <details><summary>Expand details 👇</summary><br/>
 
-    Our continuous integration (CI) testing runs [a number of checks](https://github.com/precimed/container_template/actions) for each pull request on [GitHub Actions](https://github.com/features/actions).
+    Our continuous integration (CI) testing runs [a number of checks](https://github.com/comorment/mtag_container/actions) for each pull request on [GitHub Actions](https://github.com/features/actions).
     You can run most of these tests locally, which is something you should do *before* opening a PR to help speed up the review process and make it easier for us.
 
-    And finally, please update the [CHANGELOG](https://github.com/precimed/container_template/blob/main/CHANGELOG.md) with notes on your contribution in the "Unreleased" section at the top.
+    And finally, please update the [CHANGELOG](https://github.com/comorment/mtag_container/blob/main/CHANGELOG.md) with notes on your contribution in the "Unreleased" section at the top.
 
-    After all of the above checks have passed, you can now open [a new GitHub pull request](https://github.com/precimed/container_template/pulls).
+    After all of the above checks have passed, you can now open [a new GitHub pull request](https://github.com/comorment/mtag_container/pulls).
     Make sure you have a clear description of the problem and the solution, and include a link to relevant issues.
 
     We look forward to reviewing your PR!