BLD+TST Simplify building

The instructions still dated from before conda was so well established

Change testing to match and test on all platforms (linux, macosx, and
Windows)

.github/workflows/python-app.yml

@@ -1,11 +1,13 @@
 name: Build Status
+
 on: [push, pull_request]
 
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
         python-version:
           - "3.6"
           - "3.7"
@@ -21,18 +23,23 @@ jobs:
     - name: Setup miniconda
       uses: conda-incubator/setup-miniconda@v2
       with:
-        miniconda-version: "latest"
-
-    - name: Build environment
+        activate-environment: test
+        python-version: ${{ matrix.python-version }}
+        auto-activate-base: false
+    - name: Install dependencies
+      shell: bash -l {0}
+      run : |
+        conda install -c bioconda -c conda-forge \
+          ngless pyrodigal megahit paladin pandas atomium tzlocal \
+          "scikit-learn<1.3.0" "joblib<1.3.0"
+        conda install pytest
+        pip install .
+    - name: Test with pytest
+      shell: bash -l {0}
       run: |
-        conda install -y mamba -n base -c conda-forge
-        PYTHON_VERSION=${{ matrix.python-version }} ./install.sh
-        source /usr/share/miniconda3/bin/activate envs/Macrel_env/
-        # Using conda/mamba to install pytest can cause other packages to be downgraded!
-        pip install pytest
+        python -m pytest macrel/tests
 
-    - name: Test Macrel
+    - name: Test Macrel CLI
+      shell: bash -l {0}
       run: |
-        source /usr/share/miniconda3/bin/activate envs/Macrel_env/
         ./run-tests.sh
-        python -m pytest macrel/tests

docs/install.md

@@ -9,17 +9,26 @@ conda install -c bioconda macrel
 
 ## Install from source
 
-If you want to use an unreleased version from Github, for example, we provide a
-script using _conda_ (in particular, using
-[bioconda](https://bioconda.github.io/) and
-[conda-forge](https://conda-forge.org/)) to install all dependencies in a
-Macrel-specific environment:
+If you want to use an unreleased version from Github, or tweak the code, we still recommend conda to manage the dependencies. You can install from source by running:
 
 ```bash
 git clone https://github.com/BigDataBiology/Macrel
 cd macrel
-./install.sh
-conda activate envs/Macrel_env
+
+conda create -n macrel_env
+conda activate macrel_env
+conda install -y \
+          ngless \
+          pyrodigal \
+          megahit \
+          paladin \
+          pandas \
+          "scikit-learn<1.3.0" \
+          "joblib<1.3.0" \
+          atomicwrites \
+          tzlocal
+
+pip install .
 ```
 
 Thereafter, to use macrel, activate this environment.