Updated test config files and automated unit tests.

Author: keshav-gandhi

.github/workflows/python-app.yml

@@ -1,53 +1,61 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# This workflow configures the environment and executes NEAT read-simulator tests using relative paths for a series of configuration files individually
+# For more information on using Python with GitHub Actions, refer to:
+# https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: NEAT unit tests
+name: NEAT Unit Tests
 
 on:
   push:
-    branches:
+    branches: [develop, main]
   pull_request:
-    branches:
-
-#jobs:
-#  build:
-#    runs-on: ubuntu-latest
-#
-#    steps:
-#      - uses: actions/checkout@v3
-#      - uses: s-weigand/[email protected]
-#        with:
-#          conda-channels: bioconda, conda-forge
-#          activate-conda: true
-#          repository: NCSA/NEAT
-#      - name: basic test
-#        run: |
-#          conda env create -f environment.yml -n test_neat
-#          conda activate test_neat
-#          poetry install
-#          neat
-#
-#      - name: run coverage tests
-#        run: |
-#          conda activate test_neat
-#          python tests/coverage_tests.py
-      
-#       - name: lint with flake8
-#         run: |
-#           conda activate neat
-#           # stop the build if there are Python syntax errors or undefined names
-#           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-#           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-#           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-#       - name: Execute test_gen_reads
-#         run: |
-#           conda activate neat
-#           cd ${{ github.workspace }}
-#           poetry install
-#           neat --log-level ERROR --no-log read-simulator -c data/test_config.yml -o test
-#       - run: echo "This job's status is ${{ job.status }}."
-#       - name: Execute seq_err_model_test
-#         run: |
-#           cd ${{ github.workspace }}
-#           neat --log-level ERROR --no-log model-seq-err -i data/baby.fastq
-#       - run: echo "This job's status is ${{ job.status }}." 
+    branches: [main]
+
+jobs:
+  detailed_test_execution:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: s-weigand/[email protected]
+        with:
+          conda-channels: [bioconda, conda-forge]
+          activate-conda: true
+          repository: NCSA/NEAT
+      - name: Environment Setup
+        run: |
+          conda env create -f environment.yml -n test_neat
+          conda activate test_neat
+          poetry install
+          cd config_template
+
+      - name: Run NEAT Simulation for config_test1
+        run: python -m neat --log-level DEBUG read-simulator -c config_test1.yml -o ../outputs/test1_read-simulator
+
+      - name: Run NEAT Simulation for config_test2
+        run: python -m neat --log-level DEBUG read-simulator -c config_test2.yml -o ../outputs/test2_read-simulator
+
+      - name: Run NEAT Simulation for config_test3
+        run: python -m neat --log-level DEBUG read-simulator -c config_test3.yml -o ../outputs/test3_read-simulator
+
+      - name: Run NEAT Simulation for config_test4
+        run: python -m neat --log-level DEBUG read-simulator -c config_test4.yml -o ../outputs/test4_read-simulator
+
+      - name: Run NEAT Simulation for config_test5
+        run: python -m neat --log-level DEBUG read-simulator -c config_test5.yml -o ../outputs/test5_read-simulator
+
+      - name: Run NEAT Simulation for config_test6
+        run: python -m neat --log-level DEBUG read-simulator -c config_test6.yml -o ../outputs/test6_read-simulator
+
+      - name: Run NEAT Simulation for config_test7
+        run: python -m neat --log-level DEBUG read-simulator -c config_test7.yml -o ../outputs/test7_read-simulator
+
+      - name: Run NEAT Simulation for config_test8
+        run: python -m neat --log-level DEBUG read-simulator -c config_test8.yml -o ../outputs/test8_read-simulator
+
+      - name: Run NEAT Simulation for config_test9
+        run: python -m neat --log-level DEBUG read-simulator -c config_test9.yml -o ../outputs/test9_read-simulator
+
+      - name: Run NEAT Simulation for config_test10
+        run: python -m neat --log-level DEBUG read-simulator -c config_test10.yml -o ../outputs/test10_read-simulator
+
+      - name: Run NEAT Simulation for config_test11
+        run: python -m neat --log-level DEBUG read-simulator -c config_test11.yml -o ../outputs/test11_read-simulator

config_template/config_test1.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very

config_template/config_test10.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very

config_template/config_test11.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very

config_template/config_test2.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very

config_template/config_test3.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very

config_template/config_test4.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very
@@ -103,7 +103,7 @@ mutation_rate: 0.01
 # Rates must be in the fourth column and be of the form "mut_rate=x.xx"
 # Rates must be between 0.00 and 0.03
 # type: string | required = no
-mutation_bed: /user/path/NEAT/data/H1N1.bed
+mutation_bed: ../data/H1N1.bed
 
 # Absolute path to GC content model generated by compute_gc.py
 # type: string | required = no | default: <NEAT_DIR>/neat/models/defaults/default_gc_bias_model.pickle.gz

config_template/config_test5.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very
@@ -69,7 +69,7 @@ input_variants: .
 # Absolute path to bed file containing reference regions that the simulation
 # should target.
 # type = string | required = no
-target_bed: /user/path/NEAT/data/H1N1.bed
+target_bed: ../data/H1N1.bed
 
 # Scalar value for coverage in regions outside the targeted bed. Example 0.5
 # would get you roughly half the coverage as the on target areas. Default is

config_template/config_test6.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very

config_template/config_test7.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very

config_template/config_test8.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very

config_template/config_test9.yml

@@ -11,7 +11,7 @@
 
 # Absolute path to input reference fasta file
 # type = string | required: yes
-reference: /user/path/NEAT/data/H1N1.fa
+reference: ../data/H1N1.fa
 
 # How to partition the reference for analysis. By default, NEAT will
 # attempt to process one contig per thread. However, if you have very