[MRG] Using Mamba in Pipelines

azure-pipelines/simple_test_framework.yml

@@ -30,33 +30,56 @@ jobs:
 
     steps:
       - bash: |
-          echo "##vso[task.prependpath]$CONDA/bin"
+              echo "##vso[task.setvariable variable=shellopts]errexit"
+        displayName: "Force exit on error (bash) "
+
+      - bash: |
+              echo "##vso[task.prependpath]$CONDA/bin"
         displayName: Add conda to PATH
 
       - bash: |
-          sudo chown -R $USER $CONDA
-          # conda update -y conda
+              sudo chown -R $USER $CONDA
+              # conda update -y conda
         displayName: updating conda and activating
 
       - bash: |
-          sh ci-helpers/install_tardis_env.sh
+              conda install mamba=0.4.0 -c conda-forge -y
+        displayName: "Install mamba"
+
+      - bash: |
+              mamba env create -f tardis_env3.yml
         displayName: "Install TARDIS env"
 
       - bash: |
-          sh ci-helpers/fetch_reference_data.sh
+              # sh ci-helpers/fetch_reference_data.sh
+              echo git clone $(ref.data.github.url) $(ref.data.home)
+              git clone $(ref.data.github.url) $(ref.data.home)
+              cd $(ref.data.home)
+              # Use the following to get the ref-data from the master;
+              git fetch origin
+              git checkout origin/master
+              # Use the following to get the ref-data from a specific pull request
+              #git fetch origin pull/20/head:update-ref
+              #git checkout update-ref
+              git lfs pull --include="atom_data/kurucz_cd23_chianti_H_He.h5" origin
+              git lfs pull --include="atom_data/chianti_He.h5" origin
+              git lfs pull --include="plasma_reference/" origin
+              git lfs pull --include="unit_test_data.h5" origin
+              echo MD5 `md5sum unit_test_data.h5`
+              cd $(tardis.build.dir)
         displayName: "Fetch Reference Data"
 
       - bash: |
-          source activate tardis
-          python setup.py build_ext --inplace
+              source activate tardis
+              python setup.py build_ext --inplace
         displayName: "TARDIS build"
 
       - bash: |
-          source activate tardis
-          pip install pytest-azurepipelines
-          pytest tardis --tardis-refdata=$(ref.data.home) --cov=tardis --cov-report=xml --cov-report=html
-
+              source activate tardis
+              pip install pytest-azurepipelines
+              pytest tardis --tardis-refdata=$(ref.data.home) --cov=tardis --cov-report=xml --cov-report=html
         displayName: "TARDIS test"
+
       - script: |
-          bash <(curl -s https://codecov.io/bash)
+                bash <(curl -s https://codecov.io/bash)
         displayName: "Upload to codecov.io"

ci-helpers/install_miniconda.sh

@@ -6,6 +6,7 @@ if test -e $HOME/miniconda/bin; then
     hash -r
     #conda update --yes conda
 
+
 else
     wget $MINICONDA_URL -O miniconda.sh
     chmod +x miniconda.sh
@@ -15,6 +16,7 @@ else
     export PATH=$HOME/miniconda/bin:$PATH
     hash -r
     conda update --yes conda
+
 fi
 
 source $HOME/miniconda/etc/profile.d/conda.sh

ci-helpers/install_tardis_env.sh

@@ -1,10 +1,23 @@
 #!/usr/bin/env bash
 cd $TARDIS_BUILD_DIR
+
+# install mamba
+if test -e $HOME/miniconda/bin/mamba; then
+    echo "Mamba installed Succesfuly"
+
+else
+    echo "Mamba not installed"
+    conda install mamba=0.4.0 -c conda-forge -y
+    echo "Installed Mamba to correct location"
+fi
+
 if test -e  $HOME/miniconda/envs/tardis; then
     echo "TARDIS env already installed.";
     # Also check for tardis_env3.yml change
 else
-   conda env create -f tardis_env3.yml
+   # conda env create -f tardis_env3.yml
+   echo "Creating TARDIS environment using Mamba"
+   mamba env create -f tardis_env3.yml
    #trouble with building due to segfault at cython (https://github.com/cython/cython/issues/2199)
    #remove if we can get normal cython through conda
 fi