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Expand Up@@ -9,6 +9,7 @@ Zarr-Python
:hidden:

getting_started
migration
tutorial
api/index
spec
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Expand Up@@ -19,4 +19,4 @@ latest GitHub main::

$ pip install git+https://github.com/zarr-developers/zarr-python.git

To work with Zarr source code in development, see `Contributing <contributing.html>`_.
To work with Zarr source code in development, see `Contributing <contributing.html>`_.
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Zarr-Python 3 Migration Guide
=============================

Zarr-Python 3 introduces a number of changes to the API, including a number
of significant breaking changes and pending deprecations.

This page provides a guide highlighting the most notable changes to help you
migrate your code from version 2 to version 3.

Compatibility target
--------------------

Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the goals motivating this refactor included:

- adding support for the Zarr V3 specification (alongside the Zarr V2 specification)
- cleaning up internal and user facing APIs
- improving performance (particularly in high latency storage environments like cloud object store)

These goals necessitated some breaking changes to the API (hence the major version update), but we have tried to maintain
backwards compatibility in the most widely used parts of the API including the `Array` and `Group` classes and the top-level
API (e.g. `zarr.open_array` and `zarr.open_group`).

Getting ready for 3.0
---------------------

Ahead of the 3.0 release, we suggest projects that depend on Zarr-Python take the following actions:

1. Pin the supported Zarr-Python version to ``zarr>=2,<3``. This is a best practice and will protect your users from any incompatibilities that may arise during the release of Zarr-Python 3.0.
2. Limit your imports from the Zarr-Python package. Most of the primary API ``zarr.*`` will be compatible in 3.0. However, the following breaking API changes are planned:
Comment thread
jhamman marked this conversation as resolved.

- ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)

@dstansbydstansbySep 8, 2024

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Suggested change
- ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
- ``zarr.numcodecs.*`` will no longer be available. These imports can be replaced by importing ``numcodecs`` directly.

We should be doing more than "suggesting", we should be providing concrete fixes/code updates!

@jhammanjhammanSep 13, 2024

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I wish it were that easy! Unfortunately, the top level namespace is littered with * imports

zarr-python/zarr/__init__.py

Line 2 in e1d98cd

fromzarr.codecsimport*

zarr-python/zarr/codecs.py

Line 2 in e1d98cd

fromnumcodecsimport*

If there is a reasonable way for us to deprecate folks using these imports, I'm all ears.

@dstansbydstansbySep 16, 2024

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Even if there isn't a reasonable way to deprecate the imports, as a minimum this migration guide should provide a complete list of all imports that are disappearing and how to replace them.

- The ``zarr.v3_api_available`` feature flag is being removed. In zarr-python v3 the v3 API is always available, so you shouldn't need to use this flag.
- The following internal modules are being removed or significantly changed. If your application relies on imports from any of the below modules, you will need to either a) modify your application to no longer rely on these imports or b) vendor the parts of the specific modules that you need.

- ``zarr.attrs``
- ``zarr.codecs``
- ``zarr.context``
- ``zarr.core``
- ``zarr.hierarchy``
- ``zarr.indexing``
- ``zarr.meta``
- ``zarr.meta_v1``
- ``zarr.storage``
- ``zarr.sync``
- ``zarr.types``
- ``zarr.util``
- ``zarr.n5``

Comment thread
jhamman marked this conversation as resolved.
3. Test that your package works with v3. You can start testing against version 3 now (pre-releases are being published to PyPI weekly).
4. Update the pin to zarr >=3

Continue using Zarr-Python 2
Comment thread
jhamman marked this conversation as resolved.
----------------------------

Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for its improvements and new features.
Security and bug fixes will be made to the 2.x series for at least 6 months following the first Zarr-Python 3 release.

If you need to use the latest Zarr-Python 2 release, you can install it with:

$ pip install "zarr==2.*"
Comment thread
jhamman marked this conversation as resolved.


Migration Guide
---------------

The following sections provide details on the most important changes in Zarr-Python 3.

Changes to the Array class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Group class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Store class
~~~~~~~~~~~~~~~~~~~~~~~~~~

Some of the biggest changes in Zarr-Python 3 are found in the `Store` class. The most notable changes to the Store API are:

1. Dropped the ``MutableMapping`` base class in favor of a custom abstract base class (``zarr.abc.store.Store``).
2. Switched to a primarily Async interface.

TODO

Miscellaneous changes
~~~~~~~~~~~~~~~~~~~~~

TODO
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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jhamman Aug 19, 2024
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Expand Up@@ -9,6 +9,7 @@ Zarr-Python
 :hidden:

 getting_started
 migration
 tutorial
 api/index
 spec
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Expand Up@@ -19,4 +19,4 @@ latest GitHub main::

 $ pip install git+https://github.com/zarr-developers/zarr-python.git

To work with Zarr source code in development, see `Contributing <contributing.html>`_.
To work with Zarr source code in development, see `Contributing <contributing.html>`_.

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docs/migration.rst

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@@ -0,0 +1,91 @@
Zarr-Python 3 Migration Guide
=============================

Zarr-Python 3 introduces a number of changes to the API, including a number
of significant breaking changes and pending deprecations.

This page provides a guide highlighting the most notable changes to help you
migrate your code from version 2 to version 3.

Compatibility target
--------------------

Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the goals motivating this refactor included:

 - adding support for the Zarr V3 specification (alongside the Zarr V2 specification)
 - cleaning up internal and user facing APIs
 - improving performance (particularly in high latency storage environments like cloud object store)

These goals necessitated some breaking changes to the API (hence the major version update), but we have tried to maintain
backwards compatibility in the most widely used parts of the API including the `Array` and `Group` classes and the top-level
API (e.g. `zarr.open_array` and `zarr.open_group`).

Getting ready for 3.0
---------------------

Ahead of the 3.0 release, we suggest projects that depend on Zarr-Python take the following actions:

1. Pin the supported Zarr-Python version to ``zarr>=2,<3``. This is a best practice and will protect your users from any incompatibilities that may arise during the release of Zarr-Python 3.0.
2. Limit your imports from the Zarr-Python package. Most of the primary API ``zarr.*`` will be compatible in 3.0. However, the following breaking API changes are planned:
Comment thread
jhamman marked this conversation as resolved.


 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
@dstansbydstansbySep 8, 2024

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Suggested change

 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
 - ``zarr.numcodecs.*`` will no longer be available. These imports can be replaced by importing ``numcodecs`` directly.
We should be doing more than "suggesting", we should be providing concrete fixes/code updates!
@jhammanjhammanSep 13, 2024

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MemberAuthor
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I wish it were that easy! Unfortunately, the top level namespace is littered with * imports
zarr-python/zarr/__init__.py

Line 2
in
e1d98cd
fromzarr.codecsimport*

zarr-python/zarr/codecs.py

Line 2
in
e1d98cd
fromnumcodecsimport*
If there is a reasonable way for us to deprecate folks using these imports, I'm all ears.
@dstansbydstansbySep 16, 2024

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Choose a reason for hiding this comment

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Even if there isn't a reasonable way to deprecate the imports, as a minimum this migration guide should provide a complete list of all imports that are disappearing and how to replace them.
 - The ``zarr.v3_api_available`` feature flag is being removed. In zarr-python v3 the v3 API is always available, so you shouldn't need to use this flag.
 - The following internal modules are being removed or significantly changed. If your application relies on imports from any of the below modules, you will need to either a) modify your application to no longer rely on these imports or b) vendor the parts of the specific modules that you need.

 - ``zarr.attrs``
 - ``zarr.codecs``
 - ``zarr.context``
 - ``zarr.core``
 - ``zarr.hierarchy``
 - ``zarr.indexing``
 - ``zarr.meta``
 - ``zarr.meta_v1``
 - ``zarr.storage``
 - ``zarr.sync``
 - ``zarr.types``
 - ``zarr.util``
 - ``zarr.n5``

Comment thread
jhamman marked this conversation as resolved.

3. Test that your package works with v3. You can start testing against version 3 now (pre-releases are being published to PyPI weekly).
4. Update the pin to zarr >=3

Continue using Zarr-Python 2
Comment thread
jhamman marked this conversation as resolved.

----------------------------

Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for its improvements and new features.
Security and bug fixes will be made to the 2.x series for at least 6 months following the first Zarr-Python 3 release.

If you need to use the latest Zarr-Python 2 release, you can install it with:

 $ pip install "zarr==2.*"
Comment thread
jhamman marked this conversation as resolved.



Migration Guide
---------------

The following sections provide details on the most important changes in Zarr-Python 3.

Changes to the Array class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Group class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Store class
~~~~~~~~~~~~~~~~~~~~~~~~~~

Some of the biggest changes in Zarr-Python 3 are found in the `Store` class. The most notable changes to the Store API are:

1. Dropped the ``MutableMapping`` base class in favor of a custom abstract base class (``zarr.abc.store.Store``).
2. Switched to a primarily Async interface.

TODO

Miscellaneous changes
~~~~~~~~~~~~~~~~~~~~~

TODO

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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jhamman Aug 19, 2024
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 :hidden:

 getting_started
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 api/index
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Expand Up@@ -19,4 +19,4 @@ latest GitHub main::

 $ pip install git+https://github.com/zarr-developers/zarr-python.git

To work with Zarr source code in development, see `Contributing <contributing.html>`_.
To work with Zarr source code in development, see `Contributing <contributing.html>`_.

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Zarr-Python 3 Migration Guide
=============================

Zarr-Python 3 introduces a number of changes to the API, including a number
of significant breaking changes and pending deprecations.

This page provides a guide highlighting the most notable changes to help you
migrate your code from version 2 to version 3.

Compatibility target
--------------------

Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the goals motivating this refactor included:

 - adding support for the Zarr V3 specification (alongside the Zarr V2 specification)
 - cleaning up internal and user facing APIs
 - improving performance (particularly in high latency storage environments like cloud object store)

These goals necessitated some breaking changes to the API (hence the major version update), but we have tried to maintain
backwards compatibility in the most widely used parts of the API including the `Array` and `Group` classes and the top-level
API (e.g. `zarr.open_array` and `zarr.open_group`).

Getting ready for 3.0
---------------------

Ahead of the 3.0 release, we suggest projects that depend on Zarr-Python take the following actions:

1. Pin the supported Zarr-Python version to ``zarr>=2,<3``. This is a best practice and will protect your users from any incompatibilities that may arise during the release of Zarr-Python 3.0.
2. Limit your imports from the Zarr-Python package. Most of the primary API ``zarr.*`` will be compatible in 3.0. However, the following breaking API changes are planned:
Comment thread
jhamman marked this conversation as resolved.


 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
@dstansbydstansbySep 8, 2024

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Suggested change

 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
 - ``zarr.numcodecs.*`` will no longer be available. These imports can be replaced by importing ``numcodecs`` directly.
We should be doing more than "suggesting", we should be providing concrete fixes/code updates!
@jhammanjhammanSep 13, 2024

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MemberAuthor
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I wish it were that easy! Unfortunately, the top level namespace is littered with * imports
zarr-python/zarr/__init__.py

Line 2
in
e1d98cd
fromzarr.codecsimport*

zarr-python/zarr/codecs.py

Line 2
in
e1d98cd
fromnumcodecsimport*
If there is a reasonable way for us to deprecate folks using these imports, I'm all ears.
@dstansbydstansbySep 16, 2024

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Even if there isn't a reasonable way to deprecate the imports, as a minimum this migration guide should provide a complete list of all imports that are disappearing and how to replace them.
 - The ``zarr.v3_api_available`` feature flag is being removed. In zarr-python v3 the v3 API is always available, so you shouldn't need to use this flag.
 - The following internal modules are being removed or significantly changed. If your application relies on imports from any of the below modules, you will need to either a) modify your application to no longer rely on these imports or b) vendor the parts of the specific modules that you need.

 - ``zarr.attrs``
 - ``zarr.codecs``
 - ``zarr.context``
 - ``zarr.core``
 - ``zarr.hierarchy``
 - ``zarr.indexing``
 - ``zarr.meta``
 - ``zarr.meta_v1``
 - ``zarr.storage``
 - ``zarr.sync``
 - ``zarr.types``
 - ``zarr.util``
 - ``zarr.n5``

Comment thread
jhamman marked this conversation as resolved.

3. Test that your package works with v3. You can start testing against version 3 now (pre-releases are being published to PyPI weekly).
4. Update the pin to zarr >=3

Continue using Zarr-Python 2
Comment thread
jhamman marked this conversation as resolved.

----------------------------

Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for its improvements and new features.
Security and bug fixes will be made to the 2.x series for at least 6 months following the first Zarr-Python 3 release.

If you need to use the latest Zarr-Python 2 release, you can install it with:

 $ pip install "zarr==2.*"
Comment thread
jhamman marked this conversation as resolved.



Migration Guide
---------------

The following sections provide details on the most important changes in Zarr-Python 3.

Changes to the Array class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Group class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Store class
~~~~~~~~~~~~~~~~~~~~~~~~~~

Some of the biggest changes in Zarr-Python 3 are found in the `Store` class. The most notable changes to the Store API are:

1. Dropped the ``MutableMapping`` base class in favor of a custom abstract base class (``zarr.abc.store.Store``).
2. Switched to a primarily Async interface.

TODO

Miscellaneous changes
~~~~~~~~~~~~~~~~~~~~~

TODO

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Expand Up@@ -9,6 +9,7 @@ Zarr-Python
 :hidden:

 getting_started
 migration
 tutorial
 api/index
 spec
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docs/installation.rst

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Expand Up@@ -19,4 +19,4 @@ latest GitHub main::

 $ pip install git+https://github.com/zarr-developers/zarr-python.git

To work with Zarr source code in development, see `Contributing <contributing.html>`_.
To work with Zarr source code in development, see `Contributing <contributing.html>`_.

91 changes: 91 additions & 0 deletions
docs/migration.rst

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Zarr-Python 3 Migration Guide
=============================

Zarr-Python 3 introduces a number of changes to the API, including a number
of significant breaking changes and pending deprecations.

This page provides a guide highlighting the most notable changes to help you
migrate your code from version 2 to version 3.

Compatibility target
--------------------

Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the goals motivating this refactor included:

 - adding support for the Zarr V3 specification (alongside the Zarr V2 specification)
 - cleaning up internal and user facing APIs
 - improving performance (particularly in high latency storage environments like cloud object store)

These goals necessitated some breaking changes to the API (hence the major version update), but we have tried to maintain
backwards compatibility in the most widely used parts of the API including the `Array` and `Group` classes and the top-level
API (e.g. `zarr.open_array` and `zarr.open_group`).

Getting ready for 3.0
---------------------

Ahead of the 3.0 release, we suggest projects that depend on Zarr-Python take the following actions:

1. Pin the supported Zarr-Python version to ``zarr>=2,<3``. This is a best practice and will protect your users from any incompatibilities that may arise during the release of Zarr-Python 3.0.
2. Limit your imports from the Zarr-Python package. Most of the primary API ``zarr.*`` will be compatible in 3.0. However, the following breaking API changes are planned:
Comment thread
jhamman marked this conversation as resolved.


 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
@dstansbydstansbySep 8, 2024

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Suggested change

 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
 - ``zarr.numcodecs.*`` will no longer be available. These imports can be replaced by importing ``numcodecs`` directly.
We should be doing more than "suggesting", we should be providing concrete fixes/code updates!
@jhammanjhammanSep 13, 2024

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I wish it were that easy! Unfortunately, the top level namespace is littered with * imports
zarr-python/zarr/__init__.py

Line 2
in
e1d98cd
fromzarr.codecsimport*

zarr-python/zarr/codecs.py

Line 2
in
e1d98cd
fromnumcodecsimport*
If there is a reasonable way for us to deprecate folks using these imports, I'm all ears.
@dstansbydstansbySep 16, 2024

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Even if there isn't a reasonable way to deprecate the imports, as a minimum this migration guide should provide a complete list of all imports that are disappearing and how to replace them.
 - The ``zarr.v3_api_available`` feature flag is being removed. In zarr-python v3 the v3 API is always available, so you shouldn't need to use this flag.
 - The following internal modules are being removed or significantly changed. If your application relies on imports from any of the below modules, you will need to either a) modify your application to no longer rely on these imports or b) vendor the parts of the specific modules that you need.

 - ``zarr.attrs``
 - ``zarr.codecs``
 - ``zarr.context``
 - ``zarr.core``
 - ``zarr.hierarchy``
 - ``zarr.indexing``
 - ``zarr.meta``
 - ``zarr.meta_v1``
 - ``zarr.storage``
 - ``zarr.sync``
 - ``zarr.types``
 - ``zarr.util``
 - ``zarr.n5``

Comment thread
jhamman marked this conversation as resolved.

3. Test that your package works with v3. You can start testing against version 3 now (pre-releases are being published to PyPI weekly).
4. Update the pin to zarr >=3

Continue using Zarr-Python 2
Comment thread
jhamman marked this conversation as resolved.

----------------------------

Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for its improvements and new features.
Security and bug fixes will be made to the 2.x series for at least 6 months following the first Zarr-Python 3 release.

If you need to use the latest Zarr-Python 2 release, you can install it with:

 $ pip install "zarr==2.*"
Comment thread
jhamman marked this conversation as resolved.



Migration Guide
---------------

The following sections provide details on the most important changes in Zarr-Python 3.

Changes to the Array class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Group class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Store class
~~~~~~~~~~~~~~~~~~~~~~~~~~

Some of the biggest changes in Zarr-Python 3 are found in the `Store` class. The most notable changes to the Store API are:

1. Dropped the ``MutableMapping`` base class in favor of a custom abstract base class (``zarr.abc.store.Store``).
2. Switched to a primarily Async interface.

TODO

Miscellaneous changes
~~~~~~~~~~~~~~~~~~~~~

TODO

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Expand Up@@ -9,6 +9,7 @@ Zarr-Python
 :hidden:

 getting_started
 migration
 tutorial
 api/index
 spec
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Expand Up@@ -19,4 +19,4 @@ latest GitHub main::

 $ pip install git+https://github.com/zarr-developers/zarr-python.git

To work with Zarr source code in development, see `Contributing <contributing.html>`_.
To work with Zarr source code in development, see `Contributing <contributing.html>`_.

91 changes: 91 additions & 0 deletions
docs/migration.rst

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,91 @@
Zarr-Python 3 Migration Guide
=============================

Zarr-Python 3 introduces a number of changes to the API, including a number
of significant breaking changes and pending deprecations.

This page provides a guide highlighting the most notable changes to help you
migrate your code from version 2 to version 3.

Compatibility target
--------------------

Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the goals motivating this refactor included:

 - adding support for the Zarr V3 specification (alongside the Zarr V2 specification)
 - cleaning up internal and user facing APIs
 - improving performance (particularly in high latency storage environments like cloud object store)

These goals necessitated some breaking changes to the API (hence the major version update), but we have tried to maintain
backwards compatibility in the most widely used parts of the API including the `Array` and `Group` classes and the top-level
API (e.g. `zarr.open_array` and `zarr.open_group`).

Getting ready for 3.0
---------------------

Ahead of the 3.0 release, we suggest projects that depend on Zarr-Python take the following actions:

1. Pin the supported Zarr-Python version to ``zarr>=2,<3``. This is a best practice and will protect your users from any incompatibilities that may arise during the release of Zarr-Python 3.0.
2. Limit your imports from the Zarr-Python package. Most of the primary API ``zarr.*`` will be compatible in 3.0. However, the following breaking API changes are planned:
Comment thread
jhamman marked this conversation as resolved.


 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
@dstansbydstansbySep 8, 2024

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Suggested change

 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
 - ``zarr.numcodecs.*`` will no longer be available. These imports can be replaced by importing ``numcodecs`` directly.
We should be doing more than "suggesting", we should be providing concrete fixes/code updates!
@jhammanjhammanSep 13, 2024

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MemberAuthor
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I wish it were that easy! Unfortunately, the top level namespace is littered with * imports
zarr-python/zarr/__init__.py

Line 2
in
e1d98cd
fromzarr.codecsimport*

zarr-python/zarr/codecs.py

Line 2
in
e1d98cd
fromnumcodecsimport*
If there is a reasonable way for us to deprecate folks using these imports, I'm all ears.
@dstansbydstansbySep 16, 2024

Copy link


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Contributor
Choose a reason for hiding this comment

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Even if there isn't a reasonable way to deprecate the imports, as a minimum this migration guide should provide a complete list of all imports that are disappearing and how to replace them.
 - The ``zarr.v3_api_available`` feature flag is being removed. In zarr-python v3 the v3 API is always available, so you shouldn't need to use this flag.
 - The following internal modules are being removed or significantly changed. If your application relies on imports from any of the below modules, you will need to either a) modify your application to no longer rely on these imports or b) vendor the parts of the specific modules that you need.

 - ``zarr.attrs``
 - ``zarr.codecs``
 - ``zarr.context``
 - ``zarr.core``
 - ``zarr.hierarchy``
 - ``zarr.indexing``
 - ``zarr.meta``
 - ``zarr.meta_v1``
 - ``zarr.storage``
 - ``zarr.sync``
 - ``zarr.types``
 - ``zarr.util``
 - ``zarr.n5``

Comment thread
jhamman marked this conversation as resolved.

3. Test that your package works with v3. You can start testing against version 3 now (pre-releases are being published to PyPI weekly).
4. Update the pin to zarr >=3

Continue using Zarr-Python 2
Comment thread
jhamman marked this conversation as resolved.

----------------------------

Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for its improvements and new features.
Security and bug fixes will be made to the 2.x series for at least 6 months following the first Zarr-Python 3 release.

If you need to use the latest Zarr-Python 2 release, you can install it with:

 $ pip install "zarr==2.*"
Comment thread
jhamman marked this conversation as resolved.



Migration Guide
---------------

The following sections provide details on the most important changes in Zarr-Python 3.

Changes to the Array class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Group class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Store class
~~~~~~~~~~~~~~~~~~~~~~~~~~

Some of the biggest changes in Zarr-Python 3 are found in the `Store` class. The most notable changes to the Store API are:

1. Dropped the ``MutableMapping`` base class in favor of a custom abstract base class (``zarr.abc.store.Store``).
2. Switched to a primarily Async interface.

TODO

Miscellaneous changes
~~~~~~~~~~~~~~~~~~~~~

TODO

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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3dbc86c

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 :hidden:

 getting_started
 migration
 tutorial
 api/index
 spec
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Expand Up@@ -19,4 +19,4 @@ latest GitHub main::

 $ pip install git+https://github.com/zarr-developers/zarr-python.git

To work with Zarr source code in development, see `Contributing <contributing.html>`_.
To work with Zarr source code in development, see `Contributing <contributing.html>`_.

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docs/migration.rst

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,91 @@
Zarr-Python 3 Migration Guide
=============================

Zarr-Python 3 introduces a number of changes to the API, including a number
of significant breaking changes and pending deprecations.

This page provides a guide highlighting the most notable changes to help you
migrate your code from version 2 to version 3.

Compatibility target
--------------------

Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the goals motivating this refactor included:

 - adding support for the Zarr V3 specification (alongside the Zarr V2 specification)
 - cleaning up internal and user facing APIs
 - improving performance (particularly in high latency storage environments like cloud object store)

These goals necessitated some breaking changes to the API (hence the major version update), but we have tried to maintain
backwards compatibility in the most widely used parts of the API including the `Array` and `Group` classes and the top-level
API (e.g. `zarr.open_array` and `zarr.open_group`).

Getting ready for 3.0
---------------------

Ahead of the 3.0 release, we suggest projects that depend on Zarr-Python take the following actions:

1. Pin the supported Zarr-Python version to ``zarr>=2,<3``. This is a best practice and will protect your users from any incompatibilities that may arise during the release of Zarr-Python 3.0.
2. Limit your imports from the Zarr-Python package. Most of the primary API ``zarr.*`` will be compatible in 3.0. However, the following breaking API changes are planned:
Comment thread
jhamman marked this conversation as resolved.


 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
@dstansbydstansbySep 8, 2024

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Suggested change

 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
 - ``zarr.numcodecs.*`` will no longer be available. These imports can be replaced by importing ``numcodecs`` directly.
We should be doing more than "suggesting", we should be providing concrete fixes/code updates!
@jhammanjhammanSep 13, 2024

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MemberAuthor
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I wish it were that easy! Unfortunately, the top level namespace is littered with * imports
zarr-python/zarr/__init__.py

Line 2
in
e1d98cd
fromzarr.codecsimport*

zarr-python/zarr/codecs.py

Line 2
in
e1d98cd
fromnumcodecsimport*
If there is a reasonable way for us to deprecate folks using these imports, I'm all ears.
@dstansbydstansbySep 16, 2024

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Even if there isn't a reasonable way to deprecate the imports, as a minimum this migration guide should provide a complete list of all imports that are disappearing and how to replace them.
 - The ``zarr.v3_api_available`` feature flag is being removed. In zarr-python v3 the v3 API is always available, so you shouldn't need to use this flag.
 - The following internal modules are being removed or significantly changed. If your application relies on imports from any of the below modules, you will need to either a) modify your application to no longer rely on these imports or b) vendor the parts of the specific modules that you need.

 - ``zarr.attrs``
 - ``zarr.codecs``
 - ``zarr.context``
 - ``zarr.core``
 - ``zarr.hierarchy``
 - ``zarr.indexing``
 - ``zarr.meta``
 - ``zarr.meta_v1``
 - ``zarr.storage``
 - ``zarr.sync``
 - ``zarr.types``
 - ``zarr.util``
 - ``zarr.n5``

Comment thread
jhamman marked this conversation as resolved.

3. Test that your package works with v3. You can start testing against version 3 now (pre-releases are being published to PyPI weekly).
4. Update the pin to zarr >=3

Continue using Zarr-Python 2
Comment thread
jhamman marked this conversation as resolved.

----------------------------

Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for its improvements and new features.
Security and bug fixes will be made to the 2.x series for at least 6 months following the first Zarr-Python 3 release.

If you need to use the latest Zarr-Python 2 release, you can install it with:

 $ pip install "zarr==2.*"
Comment thread
jhamman marked this conversation as resolved.



Migration Guide
---------------

The following sections provide details on the most important changes in Zarr-Python 3.

Changes to the Array class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Group class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Store class
~~~~~~~~~~~~~~~~~~~~~~~~~~

Some of the biggest changes in Zarr-Python 3 are found in the `Store` class. The most notable changes to the Store API are:

1. Dropped the ``MutableMapping`` base class in favor of a custom abstract base class (``zarr.abc.store.Store``).
2. Switched to a primarily Async interface.

TODO

Miscellaneous changes
~~~~~~~~~~~~~~~~~~~~~

TODO

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Apply suggestions from code review


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 getting_started
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Expand Up@@ -19,4 +19,4 @@ latest GitHub main::

 $ pip install git+https://github.com/zarr-developers/zarr-python.git

To work with Zarr source code in development, see `Contributing <contributing.html>`_.
To work with Zarr source code in development, see `Contributing <contributing.html>`_.

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Original file line numberDiff line numberDiff line change
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Zarr-Python 3 Migration Guide
=============================

Zarr-Python 3 introduces a number of changes to the API, including a number
of significant breaking changes and pending deprecations.

This page provides a guide highlighting the most notable changes to help you
migrate your code from version 2 to version 3.

Compatibility target
--------------------

Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the goals motivating this refactor included:

 - adding support for the Zarr V3 specification (alongside the Zarr V2 specification)
 - cleaning up internal and user facing APIs
 - improving performance (particularly in high latency storage environments like cloud object store)

These goals necessitated some breaking changes to the API (hence the major version update), but we have tried to maintain
backwards compatibility in the most widely used parts of the API including the `Array` and `Group` classes and the top-level
API (e.g. `zarr.open_array` and `zarr.open_group`).

Getting ready for 3.0
---------------------

Ahead of the 3.0 release, we suggest projects that depend on Zarr-Python take the following actions:

1. Pin the supported Zarr-Python version to ``zarr>=2,<3``. This is a best practice and will protect your users from any incompatibilities that may arise during the release of Zarr-Python 3.0.
2. Limit your imports from the Zarr-Python package. Most of the primary API ``zarr.*`` will be compatible in 3.0. However, the following breaking API changes are planned:
Comment thread
jhamman marked this conversation as resolved.


 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
@dstansbydstansbySep 8, 2024

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Suggested change

 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
 - ``zarr.numcodecs.*`` will no longer be available. These imports can be replaced by importing ``numcodecs`` directly.
We should be doing more than "suggesting", we should be providing concrete fixes/code updates!
@jhammanjhammanSep 13, 2024

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I wish it were that easy! Unfortunately, the top level namespace is littered with * imports
zarr-python/zarr/__init__.py

Line 2
in
e1d98cd
fromzarr.codecsimport*

zarr-python/zarr/codecs.py

Line 2
in
e1d98cd
fromnumcodecsimport*
If there is a reasonable way for us to deprecate folks using these imports, I'm all ears.
@dstansbydstansbySep 16, 2024

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Even if there isn't a reasonable way to deprecate the imports, as a minimum this migration guide should provide a complete list of all imports that are disappearing and how to replace them.
 - The ``zarr.v3_api_available`` feature flag is being removed. In zarr-python v3 the v3 API is always available, so you shouldn't need to use this flag.
 - The following internal modules are being removed or significantly changed. If your application relies on imports from any of the below modules, you will need to either a) modify your application to no longer rely on these imports or b) vendor the parts of the specific modules that you need.

 - ``zarr.attrs``
 - ``zarr.codecs``
 - ``zarr.context``
 - ``zarr.core``
 - ``zarr.hierarchy``
 - ``zarr.indexing``
 - ``zarr.meta``
 - ``zarr.meta_v1``
 - ``zarr.storage``
 - ``zarr.sync``
 - ``zarr.types``
 - ``zarr.util``
 - ``zarr.n5``

Comment thread
jhamman marked this conversation as resolved.

3. Test that your package works with v3. You can start testing against version 3 now (pre-releases are being published to PyPI weekly).
4. Update the pin to zarr >=3

Continue using Zarr-Python 2
Comment thread
jhamman marked this conversation as resolved.

----------------------------

Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for its improvements and new features.
Security and bug fixes will be made to the 2.x series for at least 6 months following the first Zarr-Python 3 release.

If you need to use the latest Zarr-Python 2 release, you can install it with:

 $ pip install "zarr==2.*"
Comment thread
jhamman marked this conversation as resolved.



Migration Guide
---------------

The following sections provide details on the most important changes in Zarr-Python 3.

Changes to the Array class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Group class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Store class
~~~~~~~~~~~~~~~~~~~~~~~~~~

Some of the biggest changes in Zarr-Python 3 are found in the `Store` class. The most notable changes to the Store API are:

1. Dropped the ``MutableMapping`` base class in favor of a custom abstract base class (``zarr.abc.store.Store``).
2. Switched to a primarily Async interface.

TODO

Miscellaneous changes
~~~~~~~~~~~~~~~~~~~~~

TODO

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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doc(v3): add start of v3 migration page


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Expand Up@@ -9,6 +9,7 @@ Zarr-Python
 :hidden:

 getting_started
 migration
 tutorial
 api/index
 spec
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Expand Up@@ -19,4 +19,4 @@ latest GitHub main::

 $ pip install git+https://github.com/zarr-developers/zarr-python.git

To work with Zarr source code in development, see `Contributing <contributing.html>`_.
To work with Zarr source code in development, see `Contributing <contributing.html>`_.

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@@ -0,0 +1,91 @@
Zarr-Python 3 Migration Guide
=============================

Zarr-Python 3 introduces a number of changes to the API, including a number
of significant breaking changes and pending deprecations.

This page provides a guide highlighting the most notable changes to help you
migrate your code from version 2 to version 3.

Compatibility target
--------------------

Zarr-Python 3 represents a major refactor of the Zarr-Python codebase. Some of the goals motivating this refactor included:

 - adding support for the Zarr V3 specification (alongside the Zarr V2 specification)
 - cleaning up internal and user facing APIs
 - improving performance (particularly in high latency storage environments like cloud object store)

These goals necessitated some breaking changes to the API (hence the major version update), but we have tried to maintain
backwards compatibility in the most widely used parts of the API including the `Array` and `Group` classes and the top-level
API (e.g. `zarr.open_array` and `zarr.open_group`).

Getting ready for 3.0
---------------------

Ahead of the 3.0 release, we suggest projects that depend on Zarr-Python take the following actions:

1. Pin the supported Zarr-Python version to ``zarr>=2,<3``. This is a best practice and will protect your users from any incompatibilities that may arise during the release of Zarr-Python 3.0.
2. Limit your imports from the Zarr-Python package. Most of the primary API ``zarr.*`` will be compatible in 3.0. However, the following breaking API changes are planned:
Comment thread
jhamman marked this conversation as resolved.


 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
@dstansbydstansbySep 8, 2024

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Suggested change

 - ``numcodecs.*`` will no longer be available in ``zarr.*``. (Suggested action: transition to importing codecs from ``numcodecs`` directly.)
 - ``zarr.numcodecs.*`` will no longer be available. These imports can be replaced by importing ``numcodecs`` directly.
We should be doing more than "suggesting", we should be providing concrete fixes/code updates!
@jhammanjhammanSep 13, 2024

Copy link


Copy Markdown

MemberAuthor
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I wish it were that easy! Unfortunately, the top level namespace is littered with * imports
zarr-python/zarr/__init__.py

Line 2
in
e1d98cd
fromzarr.codecsimport*

zarr-python/zarr/codecs.py

Line 2
in
e1d98cd
fromnumcodecsimport*
If there is a reasonable way for us to deprecate folks using these imports, I'm all ears.
@dstansbydstansbySep 16, 2024

Copy link


Copy Markdown

Contributor
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Even if there isn't a reasonable way to deprecate the imports, as a minimum this migration guide should provide a complete list of all imports that are disappearing and how to replace them.
 - The ``zarr.v3_api_available`` feature flag is being removed. In zarr-python v3 the v3 API is always available, so you shouldn't need to use this flag.
 - The following internal modules are being removed or significantly changed. If your application relies on imports from any of the below modules, you will need to either a) modify your application to no longer rely on these imports or b) vendor the parts of the specific modules that you need.

 - ``zarr.attrs``
 - ``zarr.codecs``
 - ``zarr.context``
 - ``zarr.core``
 - ``zarr.hierarchy``
 - ``zarr.indexing``
 - ``zarr.meta``
 - ``zarr.meta_v1``
 - ``zarr.storage``
 - ``zarr.sync``
 - ``zarr.types``
 - ``zarr.util``
 - ``zarr.n5``

Comment thread
jhamman marked this conversation as resolved.

3. Test that your package works with v3. You can start testing against version 3 now (pre-releases are being published to PyPI weekly).
4. Update the pin to zarr >=3

Continue using Zarr-Python 2
Comment thread
jhamman marked this conversation as resolved.

----------------------------

Zarr-Python 2.x is still available, though we recommend migrating to Zarr-Python 3 for its improvements and new features.
Security and bug fixes will be made to the 2.x series for at least 6 months following the first Zarr-Python 3 release.

If you need to use the latest Zarr-Python 2 release, you can install it with:

 $ pip install "zarr==2.*"
Comment thread
jhamman marked this conversation as resolved.



Migration Guide
---------------

The following sections provide details on the most important changes in Zarr-Python 3.

Changes to the Array class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Group class
~~~~~~~~~~~~~~~~~~~~~~~~~~

1. Disallow direct construction

Changes to the Store class
~~~~~~~~~~~~~~~~~~~~~~~~~~

Some of the biggest changes in Zarr-Python 3 are found in the `Store` class. The most notable changes to the Store API are:

1. Dropped the ``MutableMapping`` base class in favor of a custom abstract base class (``zarr.abc.store.Store``).
2. Switched to a primarily Async interface.

TODO

Miscellaneous changes
~~~~~~~~~~~~~~~~~~~~~

TODO