Documentation Fixes

.github/workflows/docs.yml

@@ -69,6 +69,7 @@ jobs:
               mkdocs-material-extensions \
               mkdocs-jupyter \
               "mistune<3.1" \
+            && pip install mkdocs-print-site-plugin \
             && git config user.name 'github-actions[bot]' \
             && git config user.email 'github-actions[bot]@users.noreply.github.com'
 

docs/docs/install.md

@@ -41,7 +41,7 @@ create an environment called "flacarray". First create the env with all
 dependencies and activate it (FIXME, add a requirements file for dev):
 
     conda create -n flacarray \
-        c_compiler numpy libflac cython meson-python
+        c_compiler numpy libflac cython meson-python pkgconfig
 
     conda activate flacarray
 
@@ -51,6 +51,11 @@ Now you can go into your local git checkout of the flacarray source and do:
 
 To build and install the package.
 
+To also work on docs, install additional packages:
+
+    conda install mkdocs mkdocstrings mkdocs-jupyter
+    pip install mkdocs-print-site-plugin
+
 ### Other Ways of Building
 
 !!! note "To-Do"

docs/mkdocs.yml

@@ -7,20 +7,31 @@ theme:
     - navigation.path
 
 plugins:
-- search
-- mkdocstrings:
-    handlers:
-      python:
-        options:
-          docstring_style: google
-          show_root_heading: true
-          heading_level: 3
-          parameter_headings: false
-          show_object_full_path: false
-          show_symbol_type_heading: true
-          show_symbol_type_toc: true
-- mkdocs-jupyter:
-    execute: false
+  - search
+  - mkdocstrings:
+      handlers:
+        python:
+          options:
+            docstring_style: google
+            show_root_heading: true
+            heading_level: 3
+            parameter_headings: false
+            show_object_full_path: false
+            show_symbol_type_heading: true
+            show_symbol_type_toc: true
+  - mkdocs-jupyter:
+      execute: false
+  - print-site:
+      add_to_navigation: true
+      add_print_site_banner: false
+      print_page_title: 'View as Single Page'
+      add_full_urls: false
+      add_table_of_contents: true
+      toc_title: "Table of Contents"
+      toc_depth: 2
+      enumerate_headings: false
+      enumerate_figures: true
+      add_cover_page: false
 
 nav:
   - Introduction: index.md

src/flacarray/tests/zarr.py

@@ -224,85 +224,85 @@ def test_array_write_read(self):
         flcarr_f64 = FlacArray.from_array(inputf64, mpi_comm=self.comm, use_threads=True)
         check_f64 = None
 
-        # tmpdir = None
-        # tmppath = None
-        # if rank == 0:
-        #     tmpdir = tempfile.TemporaryDirectory()
-        #     tmppath = tmpdir.name
-        # if self.comm is not None:
-        #     tmppath = self.comm.bcast(tmppath, root=0)
-
-        # i32_file = os.path.join(tmppath, "data_i32.zarr")
-        # with ZarrGroup(i32_file, mode="w", comm=self.comm) as zf:
-        #     flcarr_i32.write_zarr(zf)
-        # if self.comm is not None:
-        #     self.comm.barrier()
-        # with ZarrGroup(i32_file, mode="r", comm=self.comm) as zf:
-        #     check_i32 = FlacArray.read_zarr(zf, mpi_comm=self.comm)
-
-        # i64_file = os.path.join(tmppath, "data_i64.zarr")
-        # with ZarrGroup(i64_file, mode="w", comm=self.comm) as zf:
-        #     flcarr_i64.write_zarr(zf)
-        # if self.comm is not None:
-        #     self.comm.barrier()
-        # with ZarrGroup(i64_file, mode="r", comm=self.comm) as zf:
-        #     check_i64 = FlacArray.read_zarr(zf, mpi_comm=self.comm)
-
-        # f32_file = os.path.join(tmppath, "data_f32.zarr")
-        # with ZarrGroup(f32_file, mode="w", comm=self.comm) as zf:
-        #     flcarr_f32.write_zarr(zf)
-        # if self.comm is not None:
-        #     self.comm.barrier()
-        # with ZarrGroup(f32_file, mode="r", comm=self.comm) as zf:
-        #     check_f32 = FlacArray.read_zarr(zf, mpi_comm=self.comm)
-
-        # f64_file = os.path.join(tmppath, "data_f64.zarr")
-        # with ZarrGroup(f64_file, mode="w", comm=self.comm) as zf:
-        #     flcarr_f64.write_zarr(zf)
-        # if self.comm is not None:
-        #     self.comm.barrier()
-        # with ZarrGroup(f64_file, mode="r", comm=self.comm) as zf:
-        #     check_f64 = FlacArray.read_zarr(zf, mpi_comm=self.comm)
-
-        # if self.comm is not None:
-        #     self.comm.barrier()
-        # del tmppath
-        # del tmpdir
-
-        # if check_i32 != flcarr_i32:
-        #     print(f"check_i32 = {check_i32}", flush=True)
-        #     print(f"flcarr_i32 = {flcarr_i32}", flush=True)
-        #     print("FAIL on i32 roundtrip to zarr", flush=True)
-        #     self.assertTrue(False)
-        # else:
-        #     output_i32 = check_i32.to_array()
-        #     if not np.array_equal(output_i32, input32):
-        #         print("FAIL on i32 zarr decompressed array check", flush=True)
-        #         self.assertTrue(False)
-
-        # if check_i64 != flcarr_i64:
-        #     print("FAIL on i64 roundtrip to zarr", flush=True)
-        #     self.assertTrue(False)
-        # else:
-        #     output_i64 = check_i64.to_array()
-        #     if not np.array_equal(output_i64, input64):
-        #         print("FAIL on i64 zarr decompressed array check", flush=True)
-        #         self.assertTrue(False)
-
-        # if check_f32 != flcarr_f32:
-        #     print("FAIL on f32 roundtrip to zarr", flush=True)
-        #     self.assertTrue(False)
-        # else:
-        #     output_f32 = check_f32.to_array()
-        #     if not np.allclose(output_f32, inputf32, rtol=1.0e-5, atol=1.0e-5):
-        #         print("FAIL on f32 zarr decompressed array check", flush=True)
-        #         self.assertTrue(False)
-
-        # if check_f64 != flcarr_f64:
-        #     print("FAIL on f64 roundtrip to zarr", flush=True)
-        #     self.assertTrue(False)
-        # else:
-        #     output_f64 = check_f64.to_array()
-        #     if not np.allclose(output_f64, inputf64, rtol=1.0e-5, atol=1.0e-5):
-        #         print("FAIL on f64 zarr decompressed array check", flush=True)
-        #         self.assertTrue(False)
+        tmpdir = None
+        tmppath = None
+        if rank == 0:
+            tmpdir = tempfile.TemporaryDirectory()
+            tmppath = tmpdir.name
+        if self.comm is not None:
+            tmppath = self.comm.bcast(tmppath, root=0)
+
+        i32_file = os.path.join(tmppath, "data_i32.zarr")
+        with ZarrGroup(i32_file, mode="w", comm=self.comm) as zf:
+            flcarr_i32.write_zarr(zf)
+        if self.comm is not None:
+            self.comm.barrier()
+        with ZarrGroup(i32_file, mode="r", comm=self.comm) as zf:
+            check_i32 = FlacArray.read_zarr(zf, mpi_comm=self.comm)
+
+        i64_file = os.path.join(tmppath, "data_i64.zarr")
+        with ZarrGroup(i64_file, mode="w", comm=self.comm) as zf:
+            flcarr_i64.write_zarr(zf)
+        if self.comm is not None:
+            self.comm.barrier()
+        with ZarrGroup(i64_file, mode="r", comm=self.comm) as zf:
+            check_i64 = FlacArray.read_zarr(zf, mpi_comm=self.comm)
+
+        f32_file = os.path.join(tmppath, "data_f32.zarr")
+        with ZarrGroup(f32_file, mode="w", comm=self.comm) as zf:
+            flcarr_f32.write_zarr(zf)
+        if self.comm is not None:
+            self.comm.barrier()
+        with ZarrGroup(f32_file, mode="r", comm=self.comm) as zf:
+            check_f32 = FlacArray.read_zarr(zf, mpi_comm=self.comm)
+
+        f64_file = os.path.join(tmppath, "data_f64.zarr")
+        with ZarrGroup(f64_file, mode="w", comm=self.comm) as zf:
+            flcarr_f64.write_zarr(zf)
+        if self.comm is not None:
+            self.comm.barrier()
+        with ZarrGroup(f64_file, mode="r", comm=self.comm) as zf:
+            check_f64 = FlacArray.read_zarr(zf, mpi_comm=self.comm)
+
+        if self.comm is not None:
+            self.comm.barrier()
+        del tmppath
+        del tmpdir
+
+        if check_i32 != flcarr_i32:
+            print(f"check_i32 = {check_i32}", flush=True)
+            print(f"flcarr_i32 = {flcarr_i32}", flush=True)
+            print("FAIL on i32 roundtrip to zarr", flush=True)
+            self.assertTrue(False)
+        else:
+            output_i32 = check_i32.to_array()
+            if not np.array_equal(output_i32, input32):
+                print("FAIL on i32 zarr decompressed array check", flush=True)
+                self.assertTrue(False)
+
+        if check_i64 != flcarr_i64:
+            print("FAIL on i64 roundtrip to zarr", flush=True)
+            self.assertTrue(False)
+        else:
+            output_i64 = check_i64.to_array()
+            if not np.array_equal(output_i64, input64):
+                print("FAIL on i64 zarr decompressed array check", flush=True)
+                self.assertTrue(False)
+
+        if check_f32 != flcarr_f32:
+            print("FAIL on f32 roundtrip to zarr", flush=True)
+            self.assertTrue(False)
+        else:
+            output_f32 = check_f32.to_array()
+            if not np.allclose(output_f32, inputf32, rtol=1.0e-5, atol=1.0e-5):
+                print("FAIL on f32 zarr decompressed array check", flush=True)
+                self.assertTrue(False)
+
+        if check_f64 != flcarr_f64:
+            print("FAIL on f64 roundtrip to zarr", flush=True)
+            self.assertTrue(False)
+        else:
+            output_f64 = check_f64.to_array()
+            if not np.allclose(output_f64, inputf64, rtol=1.0e-5, atol=1.0e-5):
+                print("FAIL on f64 zarr decompressed array check", flush=True)
+                self.assertTrue(False)