Repository: phac-nml/staramr (language: python)

Issue:
Bioconda channel order
This may be something specific to my configuration, but wanted to point out in case it helps anyone else.

I was having an issue installing a standalone staramr environment (for 0.9.1 or 0.7.2) with the command as suggested:
`mamba create -c bioconda -c conda-forge -c defaults --name staramr staramr==0.7.2 pandas==1.1.5 mlst==2.19.0`

This would result in the mamba error:
Encountered problems while solving:
  - package staramr-0.7.2-py_0 requires biopython >=1.70, but none of the providers can be installed

I read elsewhere that bioconda is strict about channel order, and if things are not installed in the order conda-forge > bioconda > defaults, it can cause issues, so I changed around the 'mamba create' command to:

`mamba create -c conda-forge -c bioconda -c defaults --name staramr staramr==0.7.2 pandas==1.1.5 mlst==2.19.0`

and was able to successfully create the environment.

Thanks for a fabulous tool!
Lenora



Discussion / hints:

Fix patch:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 143d875..d4ffefc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,7 @@
+# Unreleased
+
+* Switched to only officially supporting Python 3.7+ due to recent incompatibilities with Python 3.6 and some Python packages (numpy, biopython, and others).
+
 # Version 0.9.1
 
 * Fixed a bug that occured when parsing some plasmid FASTA record IDs ([PR 159](https://github.com/phac-nml/staramr/pull/159)).
diff --git a/README.md b/README.md
index 0d466d3..a92f438 100644
--- a/README.md
+++ b/README.md
@@ -156,33 +156,33 @@ staramr db restore-default
 
 ## Bioconda
 
+
+### Separate conda environment
+
 The easiest way to install `staramr` is through [Bioconda][bioconda] (we recommend using [mamba](https://mamba.readthedocs.io/) as an alternative to `conda`).
 
 ```bash
 conda install mamba # Install mamba to make it easier to install later dependencies
-mamba install -c bioconda -c conda-forge -c defaults staramr==0.7.2 pandas==1.1.5 mlst==2.19.0
+mamba create -c conda-forge -c bioconda -c defaults --name staramr staramr
 ```
 
-This will install the `staramr` Python package at version `0.7.2` (replace with whichever version you wish to install). Bioconda will install all necessary dependencies and databases (use `pandas==1.1.5` and `mlst==2.19.0` to solve issues installing the correct dependency versions). Once this is complete you can run:
+This will install the `staramr` software at the most recent version within the conda environment named `staramr`. Bioconda will install all necessary dependencies and databases. Once this is complete you can run:
 
 ```bash
+conda activte staramr # Activate conda environment
 staramr --help
 ```
 
-If you wish to use `staramr` in an isolated environment (in case dependencies conflict) you may alternatively install with:
-
-```bash
-conda install mamba # Install mamba to make it easier to install later dependencies
-mamba create -c bioconda -c conda-forge -c defaults --name staramr staramr==0.7.2 pandas==1.1.5 mlst==2.19.0
-```
+### Same conda environment
 
-To run `staramr` in this case, you must first activate the environment.  That is:
+If, instead, you wish to install `staramr` to the current conda environment you can run:
 
 ```bash
-source activate staramr
-staramr --help
+mamba install -c conda-forge -c bioconda -c defaults staramr
 ```
 
+You should now be able to run `staramr --help` and recieve a usage statement.
+
 ## PyPI/Pip
 
 You can also install `staramr` from [PyPI][pypi-staramr] using `pip`:
@@ -229,7 +229,7 @@ staramr db restore-default
 
 ## Dependencies
 
-* Python 3.6+
+* Python 3.7+
 * BLAST+
 * Git
 * MLST


Test patch:
diff --git a/.github/workflows/ci-test.yml b/.github/workflows/ci-test.yml
index 872b2f0..1d1e75b 100644
--- a/.github/workflows/ci-test.yml
+++ b/.github/workflows/ci-test.yml
@@ -24,12 +24,8 @@ jobs:
       fail-fast: False
       matrix:
         include:
-          - python-version: "3.6"
-            pandas-version: "0.23.0"
-            other-packages: "GitPython"
-          - python-version: "3.10"
-            pandas-version: "1.4.2"
-            other-packages: ""
+          - python-version: "3.7"
+            other-packages: "mlst 'numpy <1.23.5' 'pandas <1.4'"
 
     steps:
       - uses: actions/checkout@v2
@@ -38,7 +34,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           miniconda-version: "latest"
-          activate-environment: foo
+          activate-environment: staramr-env
           python-version: ${{ matrix.python-version }}
 
       - name: Install conda packages
@@ -50,7 +46,7 @@ jobs:
           conda config --add channels conda-forge
           conda config --add channels bioconda
           conda install mamba
-          mamba install blast git mlst pandas==${{ matrix.pandas-version }} ${{ matrix.other-packages }} -y
+          mamba install Cython blast git ${{ matrix.other-packages }} -y
 
       - name: Setup python packages
         shell: bash -l {0}