Update pip / CLI

.github/workflows/CI.yaml

@@ -3,81 +3,61 @@ name: CI
 on:
   push:
     branches:
-      - "build_release_1"
       - "master"
   pull_request:
     branches:
       - "master"
-  schedule:
-    # Nightly tests run on master by default:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "0 0 * * *"
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
 
 jobs:
-  test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
+  tests:
+    runs-on: ${{ matrix.OS }}-latest
+    name: "tests"
     strategy:
+      fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.6, 3.7, 3.8]
+        os: ['ubuntu', 'macos']
+        python-version:
+          - 3.9
 
     steps:
       - uses: actions/checkout@v2
 
-      - name: Additional info about the build
-        shell: bash
-        run: |
-          uname -a
-          df -h
-          ulimit -a
-
-      # More info on options: https://github.com/goanpeca/setup-miniconda
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: ${{ matrix.python-version }}
-          environment-file: devtools/conda-envs/test_env.yaml
+            auto-update-conda: true
+            use-mamba: true
+            python-version: ${{ matrix.python-version }}
+            miniforge-variant: Mambaforge
 
-          channels: conda-forge,defaults
 
-          activate-environment: test
-          auto-update-conda: truea
-          auto-activate-base: false
-          show-channel-urls: true
+      - name: "Install"
+        run: pip install -e .
 
-      - name: Install package
-
-        # conda setup requires this special shell
-        shell: bash -l {0}
+      - name: "Test imports"
         run: |
-          python -m pip install . --no-deps
-          conda list
-
-      - name: Run tests
-
-        # conda setup requires this special shell
-        shell: bash -l {0}
-
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import ensembler"
+      - name: "Environment Information"
         run: |
-          pytest  -v --cov=ensembler --cov-report=xml --color=yes ensembler/tests/
-
-      - name: Run example notebooks
-
-        # conda setup requires this special shell
-        shell: bash -l {0}
-
-        continue-on-error: true
-
+          mamba info -a
+          mamba list
+      - name: "Run tests"
         run: |
-          # add --ignore=XXX here to ignore file XXX
-          PYTEST_ARGS+=" --nbval-lax "
-          pytest $PYTEST_ARGS examples/
-
-      - name: CodeCov
-        uses: codecov/codecov-action@v1
+          pytest -v --cov=ensembler --cov-report=xml
+      - name: codecovg
+        if: ${{ github.repository == 'rinikerlab/ensembler' && github.event != 'schedule'}}
+        uses: codecov/codecov-action@v3
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
-          flags: unittests
-          name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-
+          env_vars: OS,PYTHON
+          fail_ci_if_error: True
+          verbose: True

.github/workflows/codeql.yml

@@ -5,8 +5,10 @@ on:
     branches: [ "master" ]
   pull_request:
     branches: [ "master" ]
-  #schedule:
-  #  - cron: "8 21 * * 6"
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
 
 jobs:
   analyze:

.github/workflows/python-package.yml

@@ -7,6 +7,10 @@ on:
   pull_request:
     branches: [ master ]
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   unix-build:
     runs-on: ubuntu-latest
@@ -33,7 +37,7 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pip install -r devtools/pip_requirements/requirements_unix.txt
+        pip install .
         pytest
 
   conda-unix-build:

.github/workflows/python-publish.yml

@@ -7,6 +7,10 @@ on:
   release:
     types: [created]
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   deploy:
 

README.md

@@ -8,8 +8,6 @@ Welcome to Ensembler
 [//]: # (Badges)
 [![GitHub Actions Build Status](https://github.com/rinikerlab/ensembler/workflows/CI/badge.svg)](https://github.com/rinikerlab/ensembler/actions?query=branch%3Amaster+workflow%3ACI)
 [![codecov](https://codecov.io/gh/rinikerlab/Ensembler/branch/master/graph/badge.svg)](https://codecov.io/gh/rinikerlab/Ensembler/branch/master)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/rinikerlab/Ensembler.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/rinikerlab/Ensembler/context:python)
-![Build package](https://github.com/rinikerlab/Ensembler/workflows/Python%20package/badge.svg)
 [![Documentation](https://img.shields.io/badge/Documentation-here-white.svg)](https://rinikerlab.github.io/Ensembler/index.html)
 
 ## Description