Release/1.0.0

.flake8

@@ -1,3 +1,3 @@
 [flake8]
-exclude = docs
+exclude = docs/*
 max-line-length = 160

.github/workflows/lint.yml

@@ -0,0 +1,64 @@
+name: mlf-core linting
+on:
+  push:
+  pull_request:
+  release:
+    types: [published]
+
+jobs:
+
+  mlf-core-lint:
+    name: Run mlf-core lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install mlf-core
+        run: pip install mlf-core
+
+      - name: Run mlf-core lint
+        run: mlf-core lint .    
+
+
+  flake8:
+    name: Run flake8
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install flake8
+        run: pip install flake8
+
+      - name: Lint with flake8
+        run: flake8 .
+
+  bandit:
+    name: Run bandit
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[ci skip]')"
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install bandit
+        run: pip install bandit
+
+      - name: Run bandit
+        run: bandit -r lcep -c .bandit.yml

.github/workflows/master_branch_protection.yml

@@ -0,0 +1,74 @@
+name: PR to master branch from patch/release branch only
+
+on:
+  pull_request:
+    branches:
+    - master
+
+jobs:
+  check_target:
+    runs-on: ubuntu-latest
+    name: Check Target branch
+    steps:
+      # PRs to the repository master branch are only ok if coming from any patch or release branch
+      - name: Check PRs
+        run: |
+          { [[ $GITHUB_HEAD_REF = *"release"* ]]; } || [[ $GITHUB_HEAD_REF == *"patch"* ]]
+
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this may not work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Hi @${{ github.event.pull_request.user.login }},
+
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            The `master` branch should always contain code from the latest release.
+            Because of this, PRs to `master` are only allowed if they come from any ${{github.event.pull_request.head.repo.full_name}} `release` or `patch` branch.
+
+            You do not need to close this PR, you can change the target branch to `development` by clicking the _"Edit"_ button at the top of this page.
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
+  check_version:
+    name: No SNAPSHOT version on master branch
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+      # PRs to the repository master branch are only ok if coming from any patch or release branch
+      - name: Install mlf-core
+        run: pip install mlf-core
+
+      - name: Check project version
+        run: |
+            PROJECTVERSION=$(mlf-core bump-version --project-version . | tail -n1)
+            echo $PROJECTVERSION;
+            if [[ $PROJECTVERSION == *"SNAPSHOT"* ]];then
+                exit -1
+            else
+                exit 0
+            fi
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this may not work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Hi @${{ github.event.pull_request.user.login }},
+
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            A version check determined that you are using a SNAPSHOT version.
+            The `master` branch should never have any SNAPSHOT versions, since only fully stable code should be on the `master` branch.
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+

.github/workflows/publish_docker.yml

@@ -21,5 +21,5 @@ jobs:
         username: mlf-core
         password: '${{ secrets.MLF_CORE_SYNC_TOKEN}}'
         registry: ghcr.io
-        tags: "latest,0.1.0-SNAPSHOT"
+        tags: "latest,1.0.0"
 

.github/workflows/publish_docs.yml

@@ -0,0 +1,38 @@
+name: Build Documentation
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Setup Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.8
+
+      - name: Install pip
+        run: |
+            python -m pip install --upgrade pip
+
+      - name: Install doc dependencies
+        run: |
+            pip install -r docs/requirements.txt
+
+      - name: Build docs
+        run: |
+            cd docs
+            make html
+
+      - name: Deploy
+        if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main'}}
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html
+

.github/workflows/sync.yml

@@ -31,4 +31,4 @@ jobs:
                token: '${{ secrets.MLF_CORE_SYNC_TOKEN }}'
 
         - name: Sync project
-          run: mlf-core sync . ${{ secrets.MLF_CORE_SYNC_TOKEN }} zethson
+          run: mlf-core --verbose sync . ${{ secrets.MLF_CORE_SYNC_TOKEN }} zethson

.github/workflows/train_cpu.yml

@@ -18,16 +18,16 @@ jobs:
         with:
           dockerfile: Dockerfile
           repository: ghcr.io/mlf-core/lcep
-          tags: 0.1.0-SNAPSHOT
+          tags: 1.0.0
           push: false
 
       - name: Setup Python
         uses: actions/setup-python@v1
         with:
-          python-version:  ${{ matrix.python }}
+          python-version:  ${{ matrix.python }} 
 
       - name: Install mlflow
         run: pip install mlflow
 
       - name: Train on the CPU
-        run: mlflow run . -P training-data='/data/train.tsv' -P test-data='/data/test.tsv'
+        run: mlflow run . -P max_epochs=2 -P training-data='/data/train.tsv' -P test-data='/data/test.tsv'

.gitignore

@@ -130,3 +130,6 @@ dmypy.json
 
 # Jetbrains IDE
 .idea/
+
+# visual studio code
+.vscode

.mlf_core.yml

@@ -2,7 +2,7 @@ domain: mlflow
 language: xgboost
 project_slug: lcep
 project_slug_no_hyphen: lcep
-template_version: '1.3.0 # <<MLF-CORE_NO_BUMP>>'
+template_version: '1.3.2 # <<MLF-CORE_NO_BUMP>>'
 template_handle: mlflow-xgboost
 github_username: mlf-core
 creator_github_username: zethson
@@ -15,5 +15,5 @@ email: lukas.heumos@posteo.net
 project_name: lcep
 project_short_description: Classifying cancerous liver samples from gene expression
   data.
-version: 0.1.0-SNAPSHOT
+version: 1.0.0
 license: MIT

AUTHORS.rst

@@ -6,6 +6,7 @@ Development Lead
 ----------------
 
 * Lukas Heumos <lukas.heumos@posteo.net>
+* Steffen Lemke <steffen.lemke@uni-tuebingen.de>
 
 Contributors
 ------------

CHANGELOG.rst

@@ -5,8 +5,23 @@ Changelog
 This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
 
-0.1.0-SNAPSHOT (2020-11-11)
----------------------------------------------
+1.0.0 (2021-03-11)
+------------------
+
+**Added**
+
+* Added new train and test dataset based on TCGA-LIHC & GTEx (liver)
+* Added optimized hyperparameters to the model
+
+**Fixed**
+
+**Dependencies**
+
+**Deprecated**
+
+
+0.1.0 (2021-03-11)
+------------------
 
 **Added**