Merge pull request #43 from davidbrochart/update_xtensor

Update xtensor-zarr=0.0.7

Author: joshmoore

environment.yml

@@ -6,16 +6,14 @@ dependencies:
   - maven
   - make
   - cmake
-  - xtensor-zarr=0.0.4
+  - xtensor-zarr >=0.0.8|=0.0.7=*_1
   - openimageio
-  - zlib
-  - blosc
   - nodejs
   - z5py >= 2.0.10
   - python == 3.7.9
   - scikit-image
   - pytest
-  - zarr >= 2.8.0
+  - zarr >= 2.8.3
   - pip
   - pandas
   - tabulate

generate_data/js/package-lock.json

@@ -1,6 +1,7 @@
 import fs from "fs";
 import p from "path";
-import { PNG } from "pngjs";
+import pkg from "pngjs";
+const { PNG } = pkg;
 
 import { openGroup, NestedArray, slice } from "zarr";
 import FSStore from "./fsstore.js";
@@ -37,7 +38,7 @@ async function generateZarrFormat(codecIds = ["gzip", "blosc", "zlib", null]) {
   const path = p.join("..", "..", "data", "js.zr");
   const img = imread(p.join("..", "..", "data", "reference_image.png"));
 
-  fs.rmSync(path, { recursive: true, force: true });
+  fs.rmdirSync(path, { recursive: true, force: true });
   const grp = await open(path);
   for (const id of codecIds) {
     const config = id ? STR_TO_COMPRESSOR[id] : null;

generate_data/js/src/index.js

@@ -82,6 +82,7 @@ endif()
 target_link_libraries(run_xtensor_zarr
     PUBLIC
     xtensor-zarr
+    xtensor-zarr-gdal
     ${CMAKE_DL_LIBS}
     ${CMAKE_THREAD_LIBS_INIT}
 )

generate_data/xtensor_zarr/CMakeLists.txt

@@ -5,5 +5,7 @@ cd "${0%/*}"
 rm -rf build
 mkdir build
 cd build
+export LDFLAGS="${LDFLAGS} -Wl,-rpath,$CONDA_PREFIX/lib -Wl,-rpath,$PWD"
+export LINKFLAGS="${LDFLAGS}"
 cmake .. -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -DCMAKE_INSTALL_LIBDIR=lib
 make run