From bdf89505a7f33a5b47233e366d34db3748c19c98 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sun, 10 Nov 2024 15:05:47 -0500
Subject: [PATCH 1/2] Fix export cache spec and fix read cached spec (#232)

* Fix export cache spec and fix read cached spec

* Update changelog
---
 CHANGELOG.md             |  4 ++++
 src/hdmf_zarr/backend.py |  7 +++++++
 src/hdmf_zarr/utils.py   | 16 +++++++++-------
 3 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dc12b091..bf89d97f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,11 +1,15 @@
 # HDMF-ZARR Changelog
 
 ## 1.0.0 (Upcoming)
+
 ### Enhancements
 * Added support for Pathlib paths. @mavaylon1 [#212](https://github.com/hdmf-dev/hdmf-zarr/pull/212)
 * Updated packages used for testing and readthedocs configuration. @mavaylon1, @rly [#214](https://github.com/hdmf-dev/hdmf-zarr/pull/214)
 * Add `force_overwite` parameter for `ZarrIO.__init__` to allow overwriting an existing file or directory. @oruebel [#229](https://github.com/hdmf-dev/hdmf-zarr/pull/229)
 
+### Bug Fixes
+* Fix reading of cached specs and caching of specs during export. @rly [#232](https://github.com/hdmf-dev/hdmf-zarr/pull/232)
+
 ## 0.9.0 (September 16, 2024)
 ### Enhancements
 * Added support for appending a dataset of references. @mavaylon1 [#203](https://github.com/hdmf-dev/hdmf-zarr/pull/203)
diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
index f320683c..726bf39e 100644
--- a/src/hdmf_zarr/backend.py
+++ b/src/hdmf_zarr/backend.py
@@ -399,6 +399,13 @@ def export(self, **kwargs):
             ckwargs['clear_cache'] = True
         super().export(**ckwargs)
         if cache_spec:
+            # add any namespaces from the src_io that have not yet been loaded
+            for namespace in src_io.manager.namespace_catalog.namespaces:
+                if namespace not in self.manager.namespace_catalog.namespaces:
+                    self.manager.namespace_catalog.add_namespace(
+                        name=namespace,
+                        namespace=src_io.manager.namespace_catalog.get_namespace(namespace)
+                    )
             self.__cache_spec()
 
     def get_written(self, builder, check_on_disk=False):
diff --git a/src/hdmf_zarr/utils.py b/src/hdmf_zarr/utils.py
index 19bf75b9..1c012a22 100644
--- a/src/hdmf_zarr/utils.py
+++ b/src/hdmf_zarr/utils.py
@@ -5,6 +5,7 @@
 import math
 import json
 import logging
+import os
 from collections import deque
 from collections.abc import Iterable
 from typing import Optional, Union, Literal, Tuple, Dict, Any
@@ -373,12 +374,12 @@ class ZarrSpecReader(SpecReader):
     Class to read format specs from Zarr
     """
 
-    @docval({'name': 'group', 'type': Group, 'doc': 'the Zarr file to read specs from'},
-            {'name': 'source', 'type': str, 'doc': 'the path spec files are relative to', 'default': '.'})
+    @docval({'name': 'group', 'type': Group, 'doc': 'the Zarr file to read specs from'})
     def __init__(self, **kwargs):
-        self.__group, source = getargs('group', 'source', kwargs)
-        super_kwargs = {'source': source}
-        super(ZarrSpecReader, self).__init__(**super_kwargs)
+        self.__group = getargs('group', kwargs)
+        source = "%s:%s" % (os.path.abspath(self.__group.store.path), self.__group.name)
+        super().__init__(source=source)
+        self.__cache = None
 
     def __read(self, path):
         s = self.__group[path][0]
@@ -391,8 +392,9 @@ def read_spec(self, spec_path):
 
     def read_namespace(self, ns_path):
         """Read a namespace from the given path"""
-        ret = self.__read(ns_path)
-        ret = ret['namespaces']
+        if self.__cache is None:
+            self.__cache = self.__read(ns_path)
+        ret = self.__cache['namespaces']
         return ret
 
 

From b69c3e0b0526c5a01d2ec217c5cfdf68da724b4b Mon Sep 17 00:00:00 2001
From: Paul Adkisson <paul.wesley.adkisson@gmail.com>
Date: Tue, 12 Nov 2024 08:25:21 +1100
Subject: [PATCH 2/2] Updated dev install instructions (#233)

---
 docs/source/installation.rst | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index 2727acfe..fc55f947 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -32,7 +32,6 @@ in a Conda environment. Normally we don't need to install ``hdmf`` directly, but
 
     conda create --name hdmf-zarr-test python=3.9
     conda activate hdmf-zarr-test
-    conda install h5py
 
     git clone --recurse-submodules https://github.com/hdmf-dev/hdmf.git
     cd hdmf