add venv for executing zarrita to CI

Author: brokkoli71

.github/workflows/ci.yml

@@ -35,8 +35,8 @@ jobs:
 
       - name: Install zarrita
         run: |
-          python -m pip install --upgrade pip
-          pip install zarrita
+          python -m venv venv_zarrita
+          venv_zarrita/bin/pip install zarrita
 
       - name: Download blosc jar
         run: |

src/test/java/dev/zarr/zarrjava/ZarrTest.java

@@ -51,54 +51,11 @@ public static void clearTestoutputFolder() throws IOException {
         Files.createDirectory(TESTOUTPUT);
     }
 
-    //@BeforeAll
-    //TODO: might be needed for Windows
-    public static void installZarritaInCondaEnv() throws IOException {
-        Process process = Runtime.getRuntime().exec("conda run -n " + CONDA_ENVIRONMENT + " pip install zarrita");
-        //Process process = Runtime.getRuntime().exec(new String[]{"/bin/bash", "-c", "conda run -n " + CONDA_ENVIRONMENT + " pip install zarrita"});
-
-        BufferedReader stdError = new BufferedReader(new InputStreamReader(process.getErrorStream()));
-        String s;
-        boolean environmentLocationNotFound = false;
-        while ((s = stdError.readLine()) != null) {
-            System.err.println(s);
-            if (s.contains("EnvironmentLocationNotFound")) {
-                environmentLocationNotFound = true;
-
-            }
-        }
-        if (environmentLocationNotFound) {
-            System.out.println("creating conda environment: " + CONDA_ENVIRONMENT);
-            process = Runtime.getRuntime().exec("conda create --name " + CONDA_ENVIRONMENT + " -y");
-            System.out.println("exec: conda create --name " + CONDA_ENVIRONMENT + " -y");
-            BufferedReader stdInput = new BufferedReader(new InputStreamReader(process.getInputStream()));
-            while ((s = stdInput.readLine()) != null) {
-                System.out.println(s);
-            }
-            stdError = new BufferedReader(new InputStreamReader(process.getErrorStream()));
-            while ((s = stdError.readLine()) != null) {
-                System.err.println(s);
-            }
-
-            process = Runtime.getRuntime().exec("conda run -n " + CONDA_ENVIRONMENT + " pip install zarrita");
-            System.out.println("exec: conda run -n " + CONDA_ENVIRONMENT + " pip install zarrita");
-
-            stdInput = new BufferedReader(new InputStreamReader(process.getInputStream()));
-            while ((s = stdInput.readLine()) != null) {
-                System.out.println(s);
-            }
-            stdError = new BufferedReader(new InputStreamReader(process.getErrorStream()));
-            while ((s = stdError.readLine()) != null) {
-                System.err.println(s);
-            }
-        }
-    }
-
     @ParameterizedTest
     @ValueSource(strings = {"blosc", "gzip", "zstd", "bytes", "transpose", "sharding", "crc32c"})
     public void testReadFromZarrita(String codec) throws IOException, ZarrException, InterruptedException {
-        String command = "zarrita/bin/python";
 
+        String command = "venv_zarrita/bin/python";
         ProcessBuilder pb = new ProcessBuilder(command, ZARRITA_WRITE_PATH.toString(), codec, TESTOUTPUT.toString());
         Process process = pb.start();
 

src/test/java/dev/zarr/zarrjava/zarrita_write.py

@@ -24,7 +24,6 @@
 
 store = zarrita.LocalStore(sys.argv[2])
 testdata = np.arange(16 * 16, dtype='int32').reshape((16, 16))
-print(f"{codec=}")
 
 a = zarrita.Array.create(
     store / 'read_from_zarrita' / codec_string,