[FIX 🔨] circleci

.circleci/config.yml

@@ -1,13 +1,140 @@
-# Use the latest 2.1 version of CircleCI pipeline process engine. See: https://circleci.com/docs/2.0/configuration-reference
+# Python CircleCI 2.0 configuration file
+#
+# Check https://circleci.com/docs/2.0/language-python/ for more details
+#
 version: 2.1
-# Use a package of configuration called an orb.
+
 orbs:
-  # Declare a dependency on the welcome-orb
-  welcome: circleci/[email protected]
-# Orchestrate or schedule a set of jobs
+  codecov: codecov/[email protected]
+
+commands:
+  gettenv:
+    description: "Get/build environment"
+    parameters:
+      env:
+        type: string
+      version:
+        type: string
+    steps:
+      - restore_cache:
+          key: conda-<< parameters.env >>-v1-{{ checksum "dev_requirements.txt" }}
+      - run:
+          name: Generate environment
+          command: |
+            if [ ! -d ~/opt/anaconda3/envs/enigma_<< parameters.env >> ]; then
+              apt-get update
+              apt-get install -yqq build-essential libsnappy-dev
+              conda create -yq -n enigma_<< parameters.env >> python=<< parameters.version >>
+              source activate enigma_<< parameters.env >>
+              pip install -r dev_requirements.txt
+            fi
+      - save_cache:
+          key: conda-<< parameters.env >>-v1-{{ checksum "dev_requirements.txt" }}
+          paths:
+              - /opt/conda/envs/enigma_<< parameters.env >>
+  rununit:
+    description: "Run unit tests for enigma"
+    parameters:
+      env:
+        type: string
+    steps:
+      - run:
+          no_output_timeout: 40m
+          command: |
+            source activate enigma_<< parameters.env >>
+            pip install -e .
+            mkdir for_testing && cd for_testing
+            cp ../setup.cfg .
+            pytest --durations=5 --cov-report term-missing --cov=enigma --doctest-modules --pyargs abagen
+            mkdir /tmp/src/coverage
+            mv .coverage /tmp/src/coverage/.coverage.<< parameters.env >>
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/coverage/.coverage.<< parameters.env >>
+
+executors:
+  conda_exec:
+    docker:
+      - image: continuumio/miniconda3
+    environment:
+      ABAGEN_DATA: /tmp/src/data
+    working_directory: /tmp/src/enigma
+
+jobs:
+  makeenv_py37:
+    executor: conda_exec
+    steps:
+      - checkout
+      - gettenv:
+          env: "py37"
+          version: "3.7"
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+              - src/enigma
+  unittest_py36:
+    executor: conda_exec
+    steps:
+      - attach_workspace:
+          at: /tmp
+      - gettenv:
+          env: "py36"
+          version: "3.6"
+      - rununit:
+          env: "py36"
+  unittest_py37:
+    executor: conda_exec
+    steps:
+      - attach_workspace:
+          at: /tmp
+      - gettenv:
+          env: "py37"
+          version: "3.7"
+      - rununit:
+          env: "py37"
+  unittest_py38:
+    executor: conda_exec
+    steps:
+      - attach_workspace:
+          at: /tmp
+      - gettenv:
+          env: "py38"
+          version: "3.8"
+      - rununit:
+          env: "py38"
+  merge_coverage:
+    executor: conda_exec
+    steps:
+      - attach_workspace:
+          at: /tmp
+      - gettenv:
+          env: "py37"
+          version: "3.7"
+      - run:
+          name: Merge coverage files
+          command: |
+            apt-get update
+            apt-get install -yqq curl
+            source activate abagen_py37
+            cd /tmp/src/coverage
+            coverage combine
+            coverage xml
+      - store_artifacts:
+          path: /tmp/src/coverage
+      - codecov/upload:
+          file: /tmp/src/coverage/coverage.xml
+
 workflows:
-  # Name the workflow "welcome"
-  welcome:
-    # Run the welcome/run job in its own container
+  version: 2.1
+  build_test:
     jobs:
-      - welcome/run
+      - makeenv_py37
+      - unittest_py36:
+      - unittest_py37:
+      - unittest_py38:
+      - merge_coverage:
+          requires:
+            - unittest_py36
+            - unittest_py37
+            - unittest_py38

.circleci/dev_requirements.txt

@@ -0,0 +1,9 @@
+-r requirements.txt
+fastparquet
+flake8
+python-snappy
+pytest>=3.6
+pytest-cov
+sphinx>=2.0
+sphinx-argparse
+sphinx_rtd_theme