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Merge branch 'development' into improve-predictions
2 parents c868867 + 94999b0 commit 38f5c1b

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Lines changed: 350 additions & 373 deletions

‎.github/workflows/dev-build.yml‎

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# This worklflow will perform following actions when the code is pushed to the development branch:
3-
# - Build the latest docker image in development which needs test to pass first.
4-
# - Push the docker image to Docker Hub under namespace - nfdi4chem with tag:dev-latest.
2+
# This workflow will perform following actions when code is pushed to the development branch:
3+
# - Run tests and linting checks (can be enabled via needs: test_and_lint)
4+
# - Build and push nmrKit Docker image with layer caching for faster builds
5+
# - Conditionally build nmr-cli image only if files in app/scripts/nmr-cli/ changed
6+
# - Push images to Docker Hub under namespace nfdi4chem with dev-latest tag
7+
# - Prevent redundant builds using concurrency control
58
#
69
# Maintainers:
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# - name: Nisha Sharma
811
# - email: nisha.sharma@uni-jena.de
912

10-
name : Dev Build, Test and Publish
13+
name : Prod Build and Publish to Dev
1114

1215
on:
1316
push:
1417
branches: [development]
1518

19+
concurrency:
20+
group: ${{ github.workflow }}-${{ github.ref }}
21+
cancel-in-progress: true
22+
1623
env:
17-
DOCKER_HUB_USERNAME : ${{ secrets.DOCKER_USERNAME }}
18-
DOCKER_HUB_PASSWORD : ${{ secrets.DOCKER_PASSWORD }}
1924
NMRKIT_REPOSITORY_NAME: nmrkit
2025
NMR_CLI_REPOSITORY_NAME: nmr-cli
2126
REPOSITORY_NAMESPACE: nfdi4chem
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RELEASE_TAG: dev-latest
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2429
jobs:
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test_and_lint:
26-
uses: NFDI4Chem/nmrkit/.github/workflows/test.yml@main
27-
28-
push_to_registry:
30+
# test_and_lint:
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# uses: NFDI4Chem/nmrkit/.github/workflows/test.yml@main
32+
build_and_push_to_registry:
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name: Push Docker image to Docker Hub
3034
runs-on: ubuntu-latest
31-
#needs: test_and_lint
35+
needs: test_and_lint
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steps:
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# Clone repository code to runner
3338
- name: Check out the repo
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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# Enable advanced Docker build features (required for caching)
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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# Authenticate with Docker Hub for image push access
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- name: Log in to Docker Hub
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uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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# Detect changes in nmr-cli folder to skip unnecessary builds
53+
- name: Check for file changes
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id: changes
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uses: dorny/paths-filter@v3
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with:
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username: ${{ env.DOCKER_HUB_USERNAME }}
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password: ${{ env.DOCKER_HUB_PASSWORD }}
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filters: |
58+
nmr-cli:
59+
- 'app/scripts/nmr-cli/**'
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# Build main nmrKit image with registry caching for faster builds
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- name: Build and push nmrKit Docker image
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uses: docker/build-push-action@v4
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uses: docker/build-push-action@v6
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with:
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context: .
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file: ./Dockerfile
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push: true
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build-args: |
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RELEASE_VERSION=dev-latest
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build-args: RELEASE_VERSION=${{ env.RELEASE_TAG }}
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tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMRKIT_REPOSITORY_NAME }}:${{ env.RELEASE_TAG }}
51-
username: ${{ env.DOCKER_HUB_USERNAME }}
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password: ${{ env.DOCKER_HUB_PASSWORD }}
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cache-from: type=registry,ref=${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMRKIT_REPOSITORY_NAME }}:buildcache
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cache-to: type=registry,ref=${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMRKIT_REPOSITORY_NAME }}:buildcache,mode=max
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# Build nmr-cli image only if files in app/scripts/nmr-cli/ changed
5474
- name: Build and push nmr-cli Docker image
55-
uses: docker/build-push-action@v4
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if: steps.changes.outputs.nmr-cli == 'true'
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uses: docker/build-push-action@v6
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with:
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context: ./app/scripts/nmr-cli/
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file: ./app/scripts/nmr-cli/Dockerfile
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push: true
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build-args: |
61-
RELEASE_VERSION=dev-latest
81+
build-args: RELEASE_VERSION=${{ env.RELEASE_TAG }}
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tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMR_CLI_REPOSITORY_NAME }}:${{ env.RELEASE_TAG }}
63-
username: ${{ env.DOCKER_HUB_USERNAME }}
64-
password: ${{ env.DOCKER_HUB_PASSWORD }}
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cache-from: type=registry,ref=${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMR_CLI_REPOSITORY_NAME }}:buildcache
84+
cache-to: type=registry,ref=${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMR_CLI_REPOSITORY_NAME }}:buildcache,mode=max

‎.github/workflows/doc-deploy.yml‎

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@@ -29,23 +29,23 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
32-
uses: actions/checkout@v3
32+
uses: actions/checkout@v4
3333
with:
3434
fetch-depth: 0 # Not needed if lastUpdated is not enabled
3535
# - uses: pnpm/action-setup@v2 # Uncomment this if you're using pnpm
3636
- name: Setup Node
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uses: actions/setup-node@v3
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uses: actions/setup-node@v4
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with:
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node-version: 18
4040
cache: npm # or pnpm / yarn
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- name: Setup Pages
42-
uses: actions/configure-pages@v3
42+
uses: actions/configure-pages@v4
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- name: Install dependencies
4444
run: npm ci # or pnpm install / yarn install
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- name: Build with VitePress
4646
run: npm run docs:build # or pnpm docs:build / yarn docs:build
4747
- name: Upload artifact
48-
uses: actions/upload-pages-artifact@v2
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uses: actions/upload-pages-artifact@v3
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with:
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path: docs/.vitepress/dist
5151

@@ -60,4 +60,4 @@ jobs:
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steps:
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- name: Deploy to GitHub Pages
6262
id: deployment
63-
uses: actions/deploy-pages@v2
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uses: actions/deploy-pages@v4

‎.github/workflows/prod-build.yml‎

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Original file line numberDiff line numberDiff line change
@@ -1,60 +1,120 @@
11

2-
# This worklflow will perform following actions when the code is pushed to main branch:
3-
# - Build the latest docker image in main which needs test to pass first.
4-
# - Push the docker image to Docker Hub under namespace - nfdi4chem with tag:[release_version].
2+
# This workflow will perform following actions when code is pushed to the main branch:
3+
# - Run tests and linting checks (can be enabled via needs: test_and_lint)
4+
# - Build and push nmrKit Docker image with layer caching for faster builds
5+
# - Conditionally build nmr-cli image only if files in app/scripts/nmr-cli/ changed
6+
# - Push images to Docker Hub under namespace nfdi4chem with latest tag
7+
# - Prevent redundant builds using concurrency control
58
#
69
# Maintainers:
710
# - name: Nisha Sharma
811
# - email: nisha.sharma@uni-jena.de
912

10-
name : Prod Build, Test and Publish
13+
name : Prod Build and Publish
1114

15+
# Runs on manual workflow_dispatch with confirmation
1216
on:
13-
release:
14-
types: [published]
17+
workflow_dispatch:
18+
inputs:
19+
confirm:
20+
description: "Type 'DEPLOY' to confirm production deployment"
21+
required: true
22+
type: string
23+
24+
concurrency:
25+
group: ${{ github.workflow }}-${{ github.ref }}
26+
cancel-in-progress: true
1527

1628
env:
17-
DOCKER_HUB_USERNAME : ${{ secrets.DOCKER_USERNAME }}
18-
DOCKER_HUB_PASSWORD : ${{ secrets.DOCKER_PASSWORD }}
19-
REPOSITORY_NAME: nmrkit
29+
NMRKIT_REPOSITORY_NAME: nmrkit
30+
NMR_CLI_REPOSITORY_NAME: nmr-cli
2031
REPOSITORY_NAMESPACE: nfdi4chem
32+
RELEASE_TAG: latest
2133

2234
jobs:
23-
push_to_registry:
24-
name: Push Docker image to Docker Hub
35+
# test_and_lint:
36+
# uses: NFDI4Chem/nmrkit/.github/workflows/test.yml@main
37+
38+
# Guard: confirm input and authorize actor
39+
guard:
40+
name: Access control and confirmation
2541
runs-on: ubuntu-latest
2642
steps:
27-
- name: Check out the repo
28-
uses: actions/checkout@v3
29-
30-
#Fetch Latest release
31-
- name: Fetch latest release
32-
id: fetch-latest-release
33-
uses: InsonusK/get-latest-release@v1.0.1
34-
with:
35-
myToken: ${{ github.token }}
36-
exclude_types: "draft"
37-
view_top: 10
38-
- name: "Print release name"
43+
- name: Validate actor and confirmation
44+
shell: bash
3945
run: |
40-
echo "tag_name: ${{ steps.fetch-latest-release.outputs.tag_name }}"
46+
echo "Actor: ${GITHUB_ACTOR}"
47+
# Confirm input (workflow_dispatch)
48+
if [[ "${{ github.event.inputs.confirm }}" != "DEPLOY" ]]; then
49+
echo "Confirmation token mismatch. Expected 'DEPLOY'."
50+
exit 1
51+
fi
4152
42-
#Login to Docker Hub
53+
# Authorize actor (comma/space separated list in secret)
54+
AUTHORIZED_ACTORS="${{ secrets.PROD_DEPLOY_AUTHORIZED_ACTORS }}"
55+
allowed=0
56+
for u in ${AUTHORIZED_ACTORS//,/ }; do
57+
if [[ "${u,,}" == "${GITHUB_ACTOR,,}" ]]; then
58+
allowed=1
59+
break
60+
fi
61+
done
62+
if [[ $allowed -ne 1 ]]; then
63+
echo "User '${GITHUB_ACTOR}' is not authorized to trigger this workflow."
64+
exit 1
65+
fi
66+
echo "Authorization check passed."
67+
68+
build_and_push_to_registry:
69+
name: Push Docker image to Docker Hub
70+
runs-on: ubuntu-latest
71+
needs: guard
72+
steps:
73+
# Clone repository code to runner
74+
- name: Check out the repo
75+
uses: actions/checkout@v4
76+
77+
# Enable advanced Docker build features (required for caching)
78+
- name: Set up Docker Buildx
79+
uses: docker/setup-buildx-action@v3
80+
81+
# Authenticate with Docker Hub for image push access
4382
- name: Log in to Docker Hub
44-
uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
83+
uses: docker/login-action@v3
4584
with:
46-
username: ${{ env.DOCKER_HUB_USERNAME }}
47-
password: ${{ env.DOCKER_HUB_PASSWORD }}
48-
49-
#Build and push Docker image
50-
- name: Build and push Docker image
51-
uses: docker/build-push-action@v4
85+
username: ${{ secrets.DOCKER_USERNAME }}
86+
password: ${{ secrets.DOCKER_PASSWORD }}
87+
88+
# Detect changes in nmr-cli folder to skip unnecessary builds
89+
- name: Check for file changes
90+
id: changes
91+
uses: dorny/paths-filter@v3
92+
with:
93+
filters: |
94+
nmr-cli:
95+
- 'app/scripts/nmr-cli/**'
96+
97+
# Build main nmrKit image with registry caching for faster builds
98+
- name: Build and push nmrKit Docker image
99+
uses: docker/build-push-action@v6
52100
with:
53101
context: .
54102
file: ./Dockerfile
55103
push: true
56-
build-args: |
57-
RELEASE_VERSION=${{ steps.fetch-latest-release.outputs.tag_name }}
58-
tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:${{ steps.fetch-latest-release.outputs.tag_name }}
59-
username: ${{ env.DOCKER_HUB_USERNAME }}
60-
password: ${{ env.DOCKER_HUB_PASSWORD }}
104+
build-args: RELEASE_VERSION=${{ env.RELEASE_TAG }}
105+
tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMRKIT_REPOSITORY_NAME }}:${{ env.RELEASE_TAG }}
106+
cache-from: type=registry,ref=${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMRKIT_REPOSITORY_NAME }}:buildcache
107+
cache-to: type=registry,ref=${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMRKIT_REPOSITORY_NAME }}:buildcache,mode=max
108+
109+
# Build nmr-cli image only if files in app/scripts/nmr-cli/ changed
110+
- name: Build and push nmr-cli Docker image
111+
if: steps.changes.outputs.nmr-cli == 'true'
112+
uses: docker/build-push-action@v6
113+
with:
114+
context: ./app/scripts/nmr-cli/
115+
file: ./app/scripts/nmr-cli/Dockerfile
116+
push: true
117+
build-args: RELEASE_VERSION=${{ env.RELEASE_TAG }}
118+
tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMR_CLI_REPOSITORY_NAME }}:${{ env.RELEASE_TAG }}
119+
cache-from: type=registry,ref=${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMR_CLI_REPOSITORY_NAME }}:buildcache
120+
cache-to: type=registry,ref=${{ env.REPOSITORY_NAMESPACE }}/${{ env.NMR_CLI_REPOSITORY_NAME }}:buildcache,mode=max

‎.github/workflows/release-please.yml‎

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2-
# This worklflow will perform following actions when the code is pushed to main branch.
3-
# - Test linting with pylint.
4-
# - Test the code with pytest.
5-
# - Trigger release-please action to create release which needs test to pass first.
6-
#
7-
# Maintainers:
8-
# - name: Nisha Sharma
9-
# - email: nisha.sharma@uni-jena.de
10-
11-
name: release-please-action
1+
name: Release Please
122

133
on:
144
push:
155
branches:
166
- main
7+
workflow_dispatch: {}
178

189
jobs:
19-
test_and_lint:
20-
uses: NFDI4Chem/nmrkit/.github/workflows/test.yml@main
21-
2210
release-please:
2311
runs-on: ubuntu-latest
24-
needs: test_and_lint
12+
permissions:
13+
contents: write
14+
pull-requests: write
2515
steps:
26-
- uses: google-github-actions/release-please-action@v3
16+
- uses: googleapis/release-please-action@v4.2.0
2717
with:
2818
release-type: python
29-
package-name: release-please-action
30-
token: ${{ secrets.PAT }}
31-
prerelease: true
19+
target-branch: main
20+
token: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/test.yml‎

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Original file line numberDiff line numberDiff line change
@@ -31,9 +31,9 @@ jobs:
3131
python-version: ["3.10"]
3232

3333
steps:
34-
- uses: actions/checkout@v3
34+
- uses: actions/checkout@v4
3535
- name: Set up Python ${{ matrix.python-version }}
36-
uses: actions/setup-python@v3
36+
uses: actions/setup-python@v5
3737
with:
3838
python-version: ${{ matrix.python-version }}
3939
- name: 'Create env file'
@@ -62,4 +62,4 @@ jobs:
6262
flake8 --per-file-ignores="__init__.py:F401" --ignore E402,E501,W503 $(git ls-files 'app/*.py') .
6363
- name: Run test
6464
run: |
65-
python3 -m pytest -p no:warnings --ignore=lwreg/lwreg/test-cli.py --ignore=lwreg/lwreg/test_lwreg.py
65+
python3 -m pytest -p no:warnings --ignore=lwreg/lwreg/test-cli.py --ignore=lwreg/lwreg/test_lwreg.py --ignore=lwreg/lwreg/test_dbutils.py

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