create driver.sh for each implementation

joshmoore · joshmoore · commit d3daa8194fe1 · 2022-10-12T11:07:52.000+02:00
diff --git a/Makefile b/Makefile
@@ -1,30 +1,46 @@
 IMPLEMENTATIONS=$(wildcard implementations/*)
 
-ifeq ($(TEST),)
+ifeq ($(TEST),) #################################################
 # If TEST is not set, by default build everything, generate
 # data for all implementations, and then run all pytests.
 
-.PHONY: test
+.PHONY: test data
 test: data
 	pytest -v -k W
 
+data: $(IMPLEMENTATIONS)
+
 else
 # Otherwise, focus on a single implementation, only generating
 # its data and using the "-k W-" keyword to limit which pytests
 # get run
 
-.PHONY: test
+.PHONY: test data
 test: implementations/$(TEST)
 	pytest -v -k W-$(TEST)
 
-endif
+data: implementations/$(TEST)
+
+endif ##########################################################
+
 
 data/reference_image.png:
 	python generate_reference_image.py
 
-.PHONY: $(IMPLEMENTATIONS)
-implementations/%: data/reference_image.png
-	bash $^/driver.sh
+define mk-impl-target
+# For each of the items in our "implementations" directory,
+# create a target which depends on the reference data and
+# calls the "driver.sh" script.
+.PHONY: $1
+$1: data/reference_image.png
+	bash $1/driver.sh
+
+# Alias in case the trailing slash is included
+.PHONE: $1/
+$1/: $1
+
+endef
+$(foreach impl,$(IMPLEMENTATIONS),$(eval $(call mk-impl-target,$(impl))))
 
 .PHONY: report
 report: data
diff --git a/implementations/.conda_driver.sh b/implementations/.conda_driver.sh
@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+#
+# This is re-usable driver code for all of the implementations
+# that make use of a conda environment file.
+#
+
+set -e
+set -o pipefail
+
+create_or_activate(){ 
+    if { conda env list | grep $ENVNAME; } >/dev/null 2>&1; then
+        echo "Using $ENVNAME"
+    else
+        echo "Creating $ENVNAME"
+        conda env create -n $ENVNAME -f $IMPL/environment.yml
+    fi
+    eval "$(conda shell.bash hook)"
+    echo "Activating $ENVNAME"
+    conda activate $ENVNAME
+}
diff --git a/implementations/js/driver.sh b/implementations/js/driver.sh
@@ -0,0 +1,12 @@
+ENVNAME=ZI_js
+
+# Standard bootstrapping
+IMPL=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+ROOT=$( dirname $IMPL)
+. $ROOT/.conda_driver.sh
+create_or_activate
+
+cd "${IMPL}"
+
+npm install
+npm start
diff --git a/implementations/js/generate_data.sh b/implementations/js/generate_data.sh
diff --git a/implementations/jzarr/driver.sh b/implementations/jzarr/driver.sh
@@ -1,10 +1,15 @@
 # cd to this directory
 # https://stackoverflow.com/a/6393573/2700168
-cd "${0%/*}"
 
-set -e
-set -u
-set -x
+ENVNAME=ZI_jzarr
+
+# Standard bootstrapping
+IMPL=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+ROOT=$( dirname $IMPL)
+. $ROOT/.conda_driver.sh
+create_or_activate
+
+cd "${IMPL}"
 
 MVN_FLAGS=${MVN_FLAGS:-"--no-transfer-progress"}
 mvn "${MVN_FLAGS}" clean package
@@ -16,4 +21,3 @@ java -cp target/jzarr-1.0.0.jar zarr_implementations.jzarr.App "$@" && {
     echo jzarr failed
     exit 2
 }
-
diff --git a/implementations/n5-java/driver.sh b/implementations/n5-java/driver.sh
@@ -0,0 +1,14 @@
+ENVNAME=ZI_n5_java
+
+# Standard bootstrapping
+IMPL=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+ROOT=$( dirname $IMPL)
+. $ROOT/.conda_driver.sh
+create_or_activate
+
+cd "${IMPL}"
+
+MVN_FLAGS=${MVN_FLAGS:-"--no-transfer-progress"}
+mvn "${MVN_FLAGS}" clean package
+
+java -cp target/n5_java-1.0.0.jar zarr_implementations.n5_java.App
diff --git a/implementations/n5-java/generate_data.sh b/implementations/n5-java/generate_data.sh
diff --git a/implementations/pyn5/driver.sh b/implementations/pyn5/driver.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+#
+#
+
+ENVNAME=ZI_pyn5
+
+# Standard bootstrapping
+IMPL=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+ROOT=$( dirname $IMPL)
+. $ROOT/.conda_driver.sh
+create_or_activate
+
+python $IMPL/generate_pyn5.py
diff --git a/implementations/pyn5/environment.yml b/implementations/pyn5/environment.yml
@@ -2,14 +2,10 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - openimageio
-  - python == 3.7.9
+  - rust
+  - maturin
+  - python
   - scikit-image
-  - pytest
-  - zarr >= 2.8.3
   - pip
-  - pandas
-  - tabulate
   - pip:
       - pyn5
-      - git+https://github.com/grlee77/zarrita.git@codec_update
diff --git a/implementations/xtensor_zarr/driver.sh b/implementations/xtensor_zarr/driver.sh
@@ -1,6 +1,14 @@
-# cd to this directory
-# https://stackoverflow.com/a/6393573/2700168
-cd "${0%/*}"
+ENVNAME=ZI_xtensor_zarr
+
+# Standard bootstrapping
+IMPL=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+ROOT=$( dirname $IMPL)
+. $ROOT/.conda_driver.sh
+create_or_activate
+
+cd "${IMPL}"
+
+set +u # Due to GDAL_DATA
 
 rm -rf build
 mkdir build
diff --git a/implementations/xtensor_zarr/environment.yml b/implementations/xtensor_zarr/environment.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - make
+  - cmake
+  - xtensor-zarr >=0.0.8|=0.0.7=*_1
diff --git a/implementations/z5py/driver.sh b/implementations/z5py/driver.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+#
+#
+
+ENVNAME=ZI_z5py
+
+# Standard bootstrapping
+IMPL=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+ROOT=$( dirname $IMPL)
+. $ROOT/.conda_driver.sh
+create_or_activate
+
+python $IMPL/generate_z5py.py
diff --git a/implementations/z5py/environment.yml b/implementations/z5py/environment.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - z5py
+  - python
+  - scikit-image
diff --git a/implementations/zarr-python/driver.sh b/implementations/zarr-python/driver.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+#
+#
+
+ENVNAME=ZI_zarr_python
+
+# Standard bootstrapping
+IMPL=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+ROOT=$( dirname $IMPL)
+. $ROOT/.conda_driver.sh
+create_or_activate
+
+python $IMPL/generate_zarr.py
diff --git a/implementations/zarr-python/environment.yml b/implementations/zarr-python/environment.yml
@@ -2,14 +2,6 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - openimageio
-  - python == 3.7.9
+  - python
   - scikit-image
-  - pytest
-  - zarr >= 2.8.3
-  - pip
-  - pandas
-  - tabulate
-  - pip:
-      - pyn5
-      - git+https://github.com/grlee77/zarrita.git@codec_update
+  - zarr
diff --git a/implementations/zarrita/driver.sh b/implementations/zarrita/driver.sh
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+#
+
+ENVNAME=ZI_zarritz
+
+# Standard bootstrapping
+IMPL=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+ROOT=$( dirname $IMPL)
+. $ROOT/.conda_driver.sh
+create_or_activate
+
+python $IMPL/generate_zarrita.py
diff --git a/implementations/zarrita/environment.yml b/implementations/zarrita/environment.yml
@@ -2,14 +2,8 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - openimageio
-  - python == 3.7.9
+  - python
   - scikit-image
-  - pytest
-  - zarr >= 2.8.3
   - pip
-  - pandas
-  - tabulate
   - pip:
-      - pyn5
       - git+https://github.com/grlee77/zarrita.git@codec_update
