[dev] (Environment): Conda updates

.github/workflows/main.yml

@@ -24,7 +24,7 @@ jobs:
     steps:
       - uses: actions/checkout@v1
       - name: Setup workflow environment
-        run: make conda-tests
+        run: make conda-install
       - name: Scripts unit-testing
         run: make all-unit-tests
       - name: Run Snakemake-workflow

Snakefile

@@ -6,7 +6,7 @@ if sys.version_info < (3, 8):
     raise SystemError("Please use Python 3.8 or later.")
 
 # Snakemake 5.14.0 at least is required
-snakemake.utils.min_version("5.14.0")
+snakemake.utils.min_version("5.20.1")
 
 include: "rules/common.smk"
 include: "rules/copy.smk"

envs/workflows.yaml

@@ -5,15 +5,19 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - conda-forge::python=3.8.2
-  - conda-forge::pytest=5.4.1
+  - conda-forge::python=3.8.5
+  - conda-forge::pytest=5.4.3
   - conda-forge::datrie=0.8.2
-  - conda-forge::git=2.26.0
-  - conda-forge::jinja2=2.11.1
+  - conda-forge::git=2.27.0
+  - conda-forge::jinja2=2.11.2
   - conda-forge::pygraphviz=1.5
-  - conda-forge::flask=1.1.1
-  - conda-forge::pandas=1.0.3
+  - conda-forge::flask=1.1.2
+  - conda-forge::pandas=1.0.5
   - conda-forge::zlib=1.2.11
-  - conda-forge::openssl=1.1.1e
+  - conda-forge::openssl=1.1.1g
   - conda-forge::networkx=2.4
-  - bioconda::snakemake=5.14.0
+  - bioconda::snakemake=5.20.1
+  - conda-forge::ipython=7.16.1
+  - conda-forge::bashlex=0.15
+  - conda-forge::black=19.10b0
+  - conda-forge::patsy=0.5.1