feat: reset all Jobs to a single pinned 2.0.0 release

.github/workflows/publish-tag.yaml

@@ -0,0 +1,51 @@
+---
+name: publish-tag
+
+# Actions that publish a set of immutable, statically-tagged images.
+#
+# Run this manually when cutting a release. The tag you give is the tag every
+# image is published with, and it must be one that has never been published
+# before - the Data Manager treats any tag other than 'latest' or 'stable' as
+# static and caches it per Kubernetes node, so a reused tag leaves some nodes
+# running the old content. See docs/versioning.md in the squonk2-jobs
+# umbrella repository.
+#
+# Note that 'informaticsmatters/vs-rdkit-base' is not built here - it is built
+# and pushed by hand, and five of the images below are FROM it. Publish the
+# matching base image before running this workflow.
+
+# -----------------
+# Control variables (GitHub Secrets)
+# -----------------
+#
+# At the GitHub 'organisation' or 'project' level you must have the following
+# GitHub 'Repository Secrets' defined (i.e. via 'Settings -> Secrets'): -
+#
+# DOCKERHUB_USERNAME
+# DOCKERHUB_TOKEN
+#
+# -----------
+# Environment (GitHub Environments)
+# -----------
+#
+# Environment         (n/a)
+
+on:
+  workflow_dispatch:
+    inputs:
+      image-tag:
+        description: The immutable image tag to build and publish (e.g. 2.0.0)
+        type: string
+        required: true
+
+jobs:
+  call-test:
+    uses: ./.github/workflows/test.yaml
+
+  call-build-with-push:
+    needs: call-test
+    uses: ./.github/workflows/build-all-with-push-option.yaml
+    secrets: inherit
+    with:
+      image-tag: ${{ inputs.image-tag }}
+      image-push: true

.github/workflows/test.yaml

@@ -27,3 +27,4 @@ jobs:
         jote --manifest manifest-silicos-it.yaml --dry-run --allow-no-tests
         jote --manifest manifest-dmpk.yaml --dry-run
         jote --manifest manifest-im-mordred.yaml --dry-run
+        jote --manifest manifest-moldb.yaml --dry-run

Dockerfile-fns

@@ -1,4 +1,4 @@
-FROM informaticsmatters/vs-rdkit-base:latest
+FROM informaticsmatters/vs-rdkit-base:2.0.0
 
 # Note:     When run by the Data Manager the uid and gid
 #           will be set according to the Project we're running against.

Dockerfile-moldb

@@ -1,4 +1,4 @@
-FROM informaticsmatters/vs-rdkit-base:latest
+FROM informaticsmatters/vs-rdkit-base:2.0.0
 
 # Note:     When run by the Data Manager the uid and gid
 #           will be set according to the Project we're running against.

Dockerfile-mordred

@@ -1,4 +1,4 @@
-FROM informaticsmatters/vs-rdkit-base:latest
+FROM informaticsmatters/vs-rdkit-base:2.0.0
 
 # Note:     When run by the Data Manager the uid and gid
 #           will be set according to the Project we're running against.

Dockerfile-oddt

@@ -1,4 +1,4 @@
-FROM informaticsmatters/vs-rdkit-base:latest
+FROM informaticsmatters/vs-rdkit-base:2.0.0
 
 # Note:     When run by the Data Manager the uid and gid
 #           will be set according to the Project we're running against.

Dockerfile-prep

@@ -1,4 +1,4 @@
-FROM informaticsmatters/vs-rdkit-base:latest
+FROM informaticsmatters/vs-rdkit-base:2.0.0
 
 # Note:     When run by the Data Manager the uid and gid
 #           will be set according to the Project we're running against.

README.md

@@ -19,12 +19,26 @@ These tools are available under the [Apache2.0 license](LICENSE).
 ## Building
 The image builds are accomplished using GitHib workflows in this repository.
 
-The `rdkit-base` image on which a number of the other images depend on is
+The `vs-rdkit-base` image on which a number of the other images depend on is
 built manually and pushed to docker hub when the RDKit release needs to be updated.
-At the moment we push the image `informaticsmatters/rdkit-base:latest`, and this is
-controlled by the dockerfile `Dockerfile-rdkit-base`.
+It is controlled by the dockerfile `Dockerfile-rdkit-base`, and is pushed with
+the release tag that the dependent images will use: -
+
+    $ IMAGE_TAG=2.0.0 docker-compose -f docker-compose-manual.yaml build
+    $ IMAGE_TAG=2.0.0 docker-compose -f docker-compose-manual.yaml push
+
+Publish it *before* running the release workflow below - `Dockerfile-fns`,
+`-moldb`, `-mordred`, `-oddt` and `-prep` are all `FROM` it and will fail to
+build without it.
 
 The other images are built automatically by the GitHub workflows, where: -
 
+- The `publish-tag` workflow, run manually, results in a series of images
+  carrying the tag you give it (e.g. `:2.0.0`). This is how releases are made:
+  the Job Definitions pin these static tags, so **a tag must never be reused**
 - Every change to the `main` branch results in a series of `:stable` images
 - Every change to the `staging` branch results in a series of `:latest` images
+
+`:stable` and `:latest` are dynamic tags, intended for development only. See
+[versioning](https://github.com/InformaticsMatters/squonk2-jobs/blob/main/docs/versioning.md)
+in the `squonk2-jobs` umbrella repository.

USER_GUIDE.md

@@ -11,7 +11,7 @@ yourself for some reason this is how...
 
 To build the container images run this:
 
-    $ IMAGE_TAG=1.0.0 docker-compose build 
+    $ IMAGE_TAG=2.0.0 docker-compose build 
 
 Or, to build using the `latest` tag: -
 

data-manager/dmpk.yaml

@@ -9,7 +9,7 @@ jobs:
     name: Estimation of absorption
     description: >-
       Estimation of absorption from t1/2 and Tmax after po administration (one-compartment)
-    version: '1.0.0'
+    version: '2.0.0'
     category: dmpk
     keywords:
     - dmpk
@@ -18,7 +18,7 @@ jobs:
     - kel
     image:
       name: informaticsmatters/vs-dmpk
-      tag: 'stable'
+      tag: '2.0.0'
       project-directory: /data
       working-directory: /data
       fix-permissions: true

data-manager/fragnet-search.yaml

@@ -20,14 +20,14 @@ jobs:
     name: Fragment network expansion
     description: >-
       Expand a set of molecules using the fragment network
-    version: '1.0.0'
+    version: '2.0.0'
     category: virtual screening
     keywords:
     - fragment-network
     - candidate-selection
     image:
       name: informaticsmatters/vs-fragnet-search
-      tag: 'stable'
+      tag: '2.0.0'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -137,15 +137,15 @@ jobs:
     name: Fragment network find synthons
     description: >-
       Find the "synthons" of a molecule
-    version: '1.0.0'
+    version: '2.0.0'
     category: virtual screening
     keywords:
     - fragment-network
     - candidate-selection
     - synthons
     image:
       name: informaticsmatters/vs-fragnet-search
-      tag: 'stable'
+      tag: '2.0.0'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -222,14 +222,14 @@ jobs:
     name: Fragment network expansion
     description: >-
       Expand a set of molecules using the fragment network
-    version: '1.0.0'
+    version: '2.0.0'
     category: virtual screening
     keywords:
     - fragment-network
     - candidate-selection
     image:
       name: informaticsmatters/vs-fragnet-search
-      tag: 'stable'
+      tag: '2.0.0'
       project-directory: /data
       working-directory: /data
       fix-permissions: true