Decoupled linting and testing, and updated badges in README.

.codecov.yml

@@ -2,20 +2,6 @@ coverage:
   round: up
   precision: 2
   status:
-    project:
-      default:
-        target: 90%
-        threshold: 2%
-        base: auto
-        flags:
-          - unit
-       # advanced
-        branches:
-          - master
-        if_not_found: error
-        if_ci_failed: error
-        informational: False
-        only_pulls: false
     patch:
       default:
         # basic

.github/workflows/lint.yml

@@ -0,0 +1,53 @@
+name: "Lint"
+
+on:
+  push:
+    branches: [master,github-actions-test]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+  pull_request:
+    branches: [master]
+    paths-ignore:
+    - 'README.md'
+    - '.deepsource.toml'
+    - '.gitignore'
+    - 'setup.py'
+
+
+jobs:
+  build:
+
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]
+        python-version: [3.9]
+        test-folder : ['tests']
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Build using Python ${{matrix.python-version}}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{matrix.python-version}}
+      - name: install dependencies [pip]
+        run:  |
+          pip install --upgrade pip setuptools wheel
+          for req in dev-requirements.txt; do
+            pip install -q -r $req
+          done
+          pip install -e .
+      - name: linting [black and isort]
+        run: |
+          black . --check
+          isort --profile black --check .
+      - name: linting [flake8]
+        run: |
+          flake8 simSPI tests

.github/workflows/test_docker.yml → .github/workflows/test.yml

@@ -1,8 +1,8 @@
-name: "Linting and Testing (Docker)"
-# https://docs.github.com/en/actions/creating-actions/creating-a-docker-container-action
+name: "Test"
+
 on:
   push:
-    branches: [master,temsim-test-in-container]
+    branches: [master,github-actions-test]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
@@ -26,17 +26,6 @@ jobs:
       - name: Check Out Repo
         uses: actions/checkout@v2
 
-      - name: dryrun
-        uses: ./docker/
-        id: dryrun
-
-      - name: linting [flake8]
-        uses: ./docker/
-        id: linting
-        with:
-          command: |
-            flake8 --config=/work/.flake8 /work/simSPI /work/tests
-
       - name: unit testing [pytest]
         uses: ./docker/
         id: testing

.github/workflows/test_singularity.yml

@@ -2,16 +2,15 @@ name: "Linting and Testing (Singularity)"
 
 on:
   push:
-    branches: [simspi-test-singularity]
+    branches: [test-singularity]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
     - '.gitignore'
     - 'setup.py'
 
-
   pull_request:
-    branches: [simspi-test-singularity]
+    branches: [test-singularity]
     paths-ignore:
     - 'README.md'
     - '.deepsource.toml'
@@ -33,12 +32,6 @@ jobs:
         with:
            singularity-version: 3.8.3
 
-      - name: linting [flake8]
-        run: >
-          singularity exec docker://${{ secrets.DOCKER_HUB_USERNAME }}/simspi:latest
-          /bin/bash /opt/entrypoint.sh
-          flake8 --config=/work/.flake8 /work/simSPI /work/tests
-
       - name: unit testing [pytest]
         run: >
           singularity exec docker://${{ secrets.DOCKER_HUB_USERNAME }}/simspi:latest

README.md

@@ -1,5 +1,6 @@
-[![Build](https://github.com/compSPI/simSPI/actions/workflows/build.yml/badge.svg)](https://github.com/compSPI/simSPI/actions/workflows/build.yml)
-[![Codecov](https://codecov.io/gh/compSPI/ioSPI/branch/master/graph/badge.svg?token=OBVOV3ZM1O)](https://codecov.io/gh/compSPI/simSPI)
+[![Test](https://github.com/compSPI/simSPI/actions/workflows/test.yml/badge.svg)](https://github.com/compSPI/simSPI/actions/workflows/test.yml)
+[![Lint](https://github.com/compSPI/simSPI/actions/workflows/lint.yml/badge.svg)](https://github.com/compSPI/simSPI/actions/workflows/lint.yml)
+[![Codecov](https://codecov.io/gh/compSPI/simSPI/branch/master/graph/badge.svg?token=OBVOV3ZM1O)](https://codecov.io/gh/compSPI/simSPI)
 [![DeepSource](https://deepsource.io/gh/compSPI/simSPI.svg/?label=active+issues&show_trend=true&token=9eFu6aig3-oXQIuhdDoYTEq-)](https://deepsource.io/gh/compSPI/simSPI/?ref=repository-badge)
 
 # simSPI
@@ -8,13 +9,20 @@ Methods and tools for simulating SPI data.
 
 # Download
 
-First create a conda environment with the required dependencies using the `enviroment.yml` file as follows:
+First download:
+
+    git clone https://github.com/compSPI/simSPI.git 
+
+Then, create a conda environment with the required dependencies using the `environment.yml` file as follows:
 
     conda env create --file environment.yml
 
-Then download:
+Finally, install simSPI in this environment:
+
+    conda activate simSPI
+    pip install -e .
 
-    git clone https://github.com/compSPI/ioSPI.git
+Alternatively, pull the simSPI container from [DockerHub](https://hub.docker.com/repository/docker/fpoitevi/simspi)
 
 # Contribute
 

dev-requirements.txt

@@ -0,0 +1,5 @@
+black
+flake8
+flake8-docstrings
+isort
+pre-commit

environment.yml

@@ -7,9 +7,6 @@ dependencies:
   - codecov
   - configparser
   - coverage
-  - flake8-black
-  - flake8-docstrings
-  - flake8-import-order
   - h5py
   - mdtraj
   - mrcfile
@@ -22,9 +19,7 @@ dependencies:
   - pytorch=1.9.0
   - pytorch3d
   - pip:
-    - black==20.8b0
     - geomstats
     - git+https://github.com/compSPI/ioSPI.git
-    - pre-commit
     - raster_geometry
     - starfile