From 7c184dc55e33e39d6bab41e88b53f7b2455c5682 Mon Sep 17 00:00:00 2001
From: Pau Andrio <andriopau@gmail.com>
Date: Mon, 4 Nov 2024 10:41:51 +0100
Subject: [PATCH] [CI/CD](linting_and_testing.yml): Update set-up micromamba.

---
 .github/workflows/linting_and_testing.yaml | 129 ---------------------
 1 file changed, 129 deletions(-)
 delete mode 100644 .github/workflows/linting_and_testing.yaml

diff --git a/.github/workflows/linting_and_testing.yaml b/.github/workflows/linting_and_testing.yaml
deleted file mode 100644
index 8469d78..0000000
--- a/.github/workflows/linting_and_testing.yaml
+++ /dev/null
@@ -1,129 +0,0 @@
-name: tests
-
-on:
-  # workflow_dispatch
-  push:
-    branches: [ master ]
-    paths-ignore:
-      - '.gitignore'
-      - '.readthedocs.yaml'
-      - 'LICENSE'
-      - 'setup.py'
-      - 'README.md'
-      - 'CITATION.cff'
-      - 'references.jsonld'
-      - '**/docs/**'
-      - '**/json_schemas/**'
-
-jobs:
-  # Name of the Job
-  lint_and_test:
-    strategy:
-      matrix:
-        os: [self-hosted]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-    runs-on: ${{ matrix.os }}
-    steps:
-      - name: Check out repository code
-        uses: actions/checkout@v4
-
-      - run: echo "Repository -> ${{ github.repository }}"
-      - run: echo "Branch -> ${{ github.ref }}"
-      - run: echo "Trigger event -> ${{ github.event_name }}"
-      - run: echo "Runner OS -> ${{ runner.os }}"
-
-
-      - name: List files in the repository
-        run: |
-          ls ${{ github.workspace }}
-
-      - name: Remove all micromamba installations
-        run: |
-          rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null
-          touch /home/user/.bash_profile
-
-      - name: provision-with-micromamba
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          generate-run-shell: true
-          post-cleanup: all
-          environment-file: .github/env.yaml
-          create-args: >-
-            python=${{ matrix.python-version }}
-            pytest
-            pytest-cov
-            pytest-html
-            flake8
-            pip
-
-      - name: Install genbadge from pip
-        shell: micromamba-shell {0}  # necessary for conda env to be active
-        run: pip install genbadge[all]
-
-      - name: List installed package versions
-        shell: micromamba-shell {0}  # necessary for conda env to be active
-        run: micromamba list
-
-      - name: Lint with flake8
-        shell: micromamba-shell {0}  # necessary for conda env to be active
-        run: |
-          # F Codes: https://flake8.pycqa.org/en/latest/user/error-codes.html
-          # E Code: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
-
-          # Workflow fails: Stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-
-          # Create directory for flake8 reports
-          mkdir -p ./reports/flake8
-
-          # Exit-zero treats all errors as warnings, workflow will not fail:
-          flake8 . --exclude=docs --ignore=C901,E226 --count --exit-zero --max-complexity=10 --max-line-length=999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt
-
-      - name: Generate Flake8 badge
-        shell: micromamba-shell {0}  # necessary for conda env to be active
-        run: |
-          genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt  --output-file ./reports/flake8/flake8badge.svg
-
-      - name: Checkout biobb_common
-        uses: actions/checkout@v4
-        with:
-          repository: bioexcel/biobb_common
-          path: './biobb_common'
-
-      - name: Run tests
-        shell: micromamba-shell {0}  # necessary for conda env to be active
-        run: |
-          # Ignoring docker and singularity tests
-          export PYTHONPATH=.:./biobb_common:$PYTHONPATH
-
-          # Create directory for tests reports
-          mkdir -p ./reports/junit
-
-          # Producction one
-          pytest biobb_cmip/test/unitests/ --cov=biobb_cmip/ --cov-report=xml --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*titration* --ignore-glob=*singularity.py --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html
-
-      - name: Generate Tests badge
-        shell: micromamba-shell {0}  # necessary for conda env to be active
-        run: |
-          genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml  --output-file ./reports/junit/testsbadge.svg
-
-      - name: Generate Coverage badge
-        shell: micromamba-shell {0}  # necessary for conda env to be active
-        run: |
-          # Create directory for flake8 reports
-          mkdir -p ./reports/coverage
-
-          coverage xml -o ./reports/coverage/coverage.xml
-          coverage html -d ./reports/coverage/
-
-          genbadge coverage --name "Coverage" --input-file ./reports/coverage/coverage.xml  --output-file ./reports/coverage/coveragebadge.svg
-
-      - name: Publish coverage report to GitHub Pages
-        uses: JamesIves/github-pages-deploy-action@v4
-        with:
-          folder: ./reports
-
-      # - name: Restore .bash_profile
-      #   run: cp ~/.bash_profile_orig ~/.bash_profile
-
-