unify tests in test.sh (#666)

Co-authored-by: Jonathan Striebel <[email protected]>

Author: leowe

.github/workflows/ci.yml

@@ -190,9 +190,6 @@ jobs:
         pip install poetry
         poetry install
 
-    - name: Decompress test data
-      run: tar -xzvf testdata/WT1_wkw.tar.gz
-
     - name: Check formatting
       run: ./format.sh check
       if: ${{ needs.changes.outputs.wkcuber == 'true' }}
@@ -204,11 +201,8 @@ jobs:
     - name: Check typing
       run: ./typecheck.sh
 
-    - name: Python tests
-      run: poetry run pytest tests
-
-    - name: CLI tests
-      run: poetry run tests/scripts/all_tests.sh
+    - name: Run tests
+      run: ./test.sh
 
     - name: Check if git is dirty
       run: |
@@ -244,18 +238,10 @@ jobs:
         pip install poetry
         poetry install
 
-    - name: Decompress test data
-      shell: bash
-      run: tar -xzvf testdata/WT1_wkw.tar.gz
-
-    - name: Python tests
-      shell: bash
-      run: poetry run pytest tests
-
-    - name: CLI tests
+    - name: Run tests
       continue-on-error: true
       shell: bash
-      run: poetry run "C:\Program Files\Git\bin\bash.EXE" --noprofile --norc tests/scripts/all_tests.sh
+      run: poetry run "C:\Program Files\Git\bin\bash.EXE" --noprofile --norc ./test.sh
 
   wkcuber_mac:
     runs-on: macos-latest
@@ -284,14 +270,8 @@ jobs:
         pip install poetry
         poetry install
 
-    - name: Decompress test data
-      run: tar -xzvf testdata/WT1_wkw.tar.gz
-
-    - name: Python tests
-      run: poetry run pytest tests
-
-    - name: CLI tests
-      run: poetry run tests/scripts/all_tests.sh
+    - name: Run tests
+      run: ./test.sh
 
   wkcuber_docker:
     needs: [cluster_tools, webknossos_linux, wkcuber_linux, wkcuber_win, wkcuber_mac]

wkcuber/test.sh

@@ -1,19 +1,71 @@
-set -euxo pipefail
-export CIRCLE_BUILD_NUM=latest
-tests/scripts/build_docker_image.sh
-tests/scripts/decompress_test_data.sh
-tests/scripts/check_formatting.sh
-tests/scripts/python_tests.sh
-tests/scripts/tiff_cubing.sh
-tests/scripts/in_memory_downsampled_cubing.sh
-tests/scripts/tile_cubing.sh
-tests/scripts/simple_tiff_cubing.sh
-tests/scripts/simple_tiff_cubing_no_compression.sh
-tests/scripts/knossos_conversion.sh
-tests/scripts/decompress_reference_mag.sh
-tests/scripts/downsampling.sh
-tests/scripts/compression_and_verification.sh
-tests/scripts/in_place_compression.sh
-tests/scripts/meta_generation.sh
-tests/scripts/simple_anisotropic_tiff_cubing.sh
-tests/scripts/anisotropic_downsampling.sh
+#!/usr/bin/env bash
+set -eEuo pipefail
+
+TEST_WKW_PATH=testdata/WT1_wkw
+TEST_WKW_ARCHIVE=testdata/WT1_wkw.tar.gz
+TEST_TIFF_PATH=testdata/tiff_mag_2_reference
+TEST_TIFF=testdata/tiff_mag_2_reference.tar.gz
+
+OUTPUT_PATH=testoutput
+SCRIPTS_BASEDIR=./tests/scripts
+
+# Cleanup
+if [ -d $OUTPUT_PATH ]; then
+  echo "Removing $OUTPUT_PATH"
+  rm -Rf $OUTPUT_PATH
+fi
+
+# Setup
+if [ ! -d $TEST_WKW_PATH ]; then
+  echo "Extracting $TEST_WKW_ARCHIVE into $TEST_WKW_PATH"
+  tar -xzvf $TEST_WKW_ARCHIVE
+fi
+
+if [ ! -d $TEST_TIFF_PATH ]; then
+  echo "Extracting $TEST_TIFF into $TEST_TIFF_PATH"
+  mkdir -p $TEST_TIFF_PATH
+  tar -xzvf $TEST_TIFF -C $TEST_TIFF_PATH
+fi
+
+# Note that pytest should be executed via `python -m`, since
+# this will ensure that the current directory is added to sys.path
+# (which is standard python behavior). This is necessary so that the imports
+# refer to the checked out (and potentially modified) code.
+poetry run python -m pytest tests
+
+poetry run sh ${SCRIPTS_BASEDIR}/tiff_cubing.sh
+poetry run sh ${SCRIPTS_BASEDIR}/meta_generation.sh
+poetry run sh ${SCRIPTS_BASEDIR}/downsampling.sh
+poetry run sh ${SCRIPTS_BASEDIR}/upsampling.sh
+rm -r $OUTPUT_PATH/tiff_upsampling
+rm -r testdata/tiff_mag_2_reference
+
+poetry run sh ${SCRIPTS_BASEDIR}/anisotropic_downsampling.sh
+poetry run sh ${SCRIPTS_BASEDIR}/compression_and_verification.sh
+rm -r $OUTPUT_PATH/tiff_compress
+rm -r $OUTPUT_PATH/tiff_compress_broken
+
+poetry run sh ${SCRIPTS_BASEDIR}/in_place_compression.sh
+rm -r $OUTPUT_PATH/tiff_compress2
+rm -r $OUTPUT_PATH/tiff_compress2.bak
+rm -r $OUTPUT_PATH/tiff
+
+poetry run sh ${SCRIPTS_BASEDIR}/tile_cubing.sh
+rm -r $OUTPUT_PATH/temca2
+
+poetry run sh ${SCRIPTS_BASEDIR}/simple_tiff_cubing.sh
+rm -r $OUTPUT_PATH/tiff2
+
+poetry run sh ${SCRIPTS_BASEDIR}/simple_tiff_cubing_no_compression.sh
+rm -r $OUTPUT_PATH/tiff3
+
+poetry run sh ${SCRIPTS_BASEDIR}/tiff_formats_cubing.sh
+rm -r $OUTPUT_PATH/tiff4
+
+poetry run sh ${SCRIPTS_BASEDIR}/knossos_conversion.sh
+rm -r $OUTPUT_PATH/knossos
+
+poetry run sh ${SCRIPTS_BASEDIR}/convert_raw.sh
+rm -r $OUTPUT_PATH/raw
+
+rm -r $OUTPUT_PATH