zarr 2.10.0 fails to load pre-existing nested files #840

Closed
#850
Closed
zarr 2.10.0 fails to load pre-existing nested files#840
#850

Description

@abred
abred
opened on Sep 28, 2021

Minimal, reproducible code sample, a copy-pastable example if possible

importnumpyasnpimportzarra=np.ones((2,2)) z=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'w')
z['test'] =az=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'r')
print(np.array(z['test']))
arr=zarr.open(zarr.NestedDirectoryStore("path/to/existing/zarr/file.zarr"), 'r')
print(np.max(arr['volumes/raw']))

output with zarr 2.10.0:
array([[1., 1.],
[1., 1.]])
0

output with zarr 2.3.0:
array([[1., 1.],
[1., 1.]])
6733

Problem description

With the current version of zarr (2.10.0) pre-existing zarr files using NestedDirectoryStore are all zero when read.
With an older version (tested with 2.3.0) the correct values are loaded.
Creating a new zarr file using NestedDirectoryStore on 2.10.0 and reading it works correctly.

Version and installation information

Please provide the following:

  • Value of zarr.__version__: '2.10.0'
  • Value of numcodecs.__version__: '0.9.1'
  • Version of Python interpreter: 3.8.11
  • Operating system (Linux/Windows/Mac): Linux
  • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip install

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      , '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" + '

      Skip to content
      zarr 2.10.0 fails to load pre-existing nested files #840
      Closed
      #850
      Closed
      zarr 2.10.0 fails to load pre-existing nested files#840
      #850
      Description
      @abred
      abred
      opened on Sep 28, 2021
      Minimal, reproducible code sample, a copy-pastable example if possible
      importnumpyasnpimportzarra=np.ones((2,2)) z=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'w')
z['test'] =az=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'r')
print(np.array(z['test']))
arr=zarr.open(zarr.NestedDirectoryStore("path/to/existing/zarr/file.zarr"), 'r')
print(np.max(arr['volumes/raw']))
      output with zarr 2.10.0:
      
array([[1., 1.],
      
[1., 1.]])
      
0
      output with zarr 2.3.0:
      
array([[1., 1.],
      
[1., 1.]])
      
6733
      Problem description
      With the current version of zarr (2.10.0) pre-existing zarr files using NestedDirectoryStore are all zero when read.
      
With an older version (tested with 2.3.0) the correct values are loaded.
      
Creating a new zarr file using NestedDirectoryStore on 2.10.0 and reading it works correctly.
      Version and installation information
      Please provide the following:
      • Value of zarr.__version__: '2.10.0'
      • Value of numcodecs.__version__: '0.9.1'
      • Version of Python interpreter: 3.8.11
      • Operating system (Linux/Windows/Mac): Linux
      • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip install
      Metadata
      Metadata
      Assignees
      No one assigned
        Labels
        No labels
        No labels
        Type
        No type
        Projects
        No projects
          Milestone
          No milestone
          Relationships
          None yet
          Development
          No branches or pull requests
          Issue actions
          
, '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('^' + ".*" + '

          Skip to content
          zarr 2.10.0 fails to load pre-existing nested files #840
          Closed
          #850
          Closed
          zarr 2.10.0 fails to load pre-existing nested files#840
          #850
          Description
          @abred
          abred
          opened on Sep 28, 2021
          Minimal, reproducible code sample, a copy-pastable example if possible
          importnumpyasnpimportzarra=np.ones((2,2)) z=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'w')
z['test'] =az=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'r')
print(np.array(z['test']))
arr=zarr.open(zarr.NestedDirectoryStore("path/to/existing/zarr/file.zarr"), 'r')
print(np.max(arr['volumes/raw']))
          output with zarr 2.10.0:
          
array([[1., 1.],
          
[1., 1.]])
          
0
          output with zarr 2.3.0:
          
array([[1., 1.],
          
[1., 1.]])
          
6733
          Problem description
          With the current version of zarr (2.10.0) pre-existing zarr files using NestedDirectoryStore are all zero when read.
          
With an older version (tested with 2.3.0) the correct values are loaded.
          
Creating a new zarr file using NestedDirectoryStore on 2.10.0 and reading it works correctly.
          Version and installation information
          Please provide the following:
          • Value of zarr.__version__: '2.10.0'
          • Value of numcodecs.__version__: '0.9.1'
          • Version of Python interpreter: 3.8.11
          • Operating system (Linux/Windows/Mac): Linux
          • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip install
          Metadata
          Metadata
          Assignees
          No one assigned
            Labels
            No labels
            No labels
            Type
            No type
            Projects
            No projects
              Milestone
              No milestone
              Relationships
              None yet
              Development
              No branches or pull requests
              Issue actions
              
, '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('^' + ".*" + '

              Skip to content
              zarr 2.10.0 fails to load pre-existing nested files #840
              Closed
              #850
              Closed
              zarr 2.10.0 fails to load pre-existing nested files#840
              #850
              Description
              @abred
              abred
              opened on Sep 28, 2021
              Minimal, reproducible code sample, a copy-pastable example if possible
              importnumpyasnpimportzarra=np.ones((2,2)) z=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'w')
z['test'] =az=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'r')
print(np.array(z['test']))
arr=zarr.open(zarr.NestedDirectoryStore("path/to/existing/zarr/file.zarr"), 'r')
print(np.max(arr['volumes/raw']))
              output with zarr 2.10.0:
              
array([[1., 1.],
              
[1., 1.]])
              
0
              output with zarr 2.3.0:
              
array([[1., 1.],
              
[1., 1.]])
              
6733
              Problem description
              With the current version of zarr (2.10.0) pre-existing zarr files using NestedDirectoryStore are all zero when read.
              
With an older version (tested with 2.3.0) the correct values are loaded.
              
Creating a new zarr file using NestedDirectoryStore on 2.10.0 and reading it works correctly.
              Version and installation information
              Please provide the following:
              • Value of zarr.__version__: '2.10.0'
              • Value of numcodecs.__version__: '0.9.1'
              • Version of Python interpreter: 3.8.11
              • Operating system (Linux/Windows/Mac): Linux
              • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip install
              Metadata
              Metadata
              Assignees
              No one assigned
                Labels
                No labels
                No labels
                Type
                No type
                Projects
                No projects
                  Milestone
                  No milestone
                  Relationships
                  None yet
                  Development
                  No branches or pull requests
                  Issue actions
                  
, '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" + '

                  Skip to content
                  zarr 2.10.0 fails to load pre-existing nested files #840
                  Closed
                  #850
                  Closed
                  zarr 2.10.0 fails to load pre-existing nested files#840
                  #850
                  Description
                  @abred
                  abred
                  opened on Sep 28, 2021
                  Minimal, reproducible code sample, a copy-pastable example if possible
                  importnumpyasnpimportzarra=np.ones((2,2)) z=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'w')
z['test'] =az=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'r')
print(np.array(z['test']))
arr=zarr.open(zarr.NestedDirectoryStore("path/to/existing/zarr/file.zarr"), 'r')
print(np.max(arr['volumes/raw']))
                  output with zarr 2.10.0:
                  
array([[1., 1.],
                  
[1., 1.]])
                  
0
                  output with zarr 2.3.0:
                  
array([[1., 1.],
                  
[1., 1.]])
                  
6733
                  Problem description
                  With the current version of zarr (2.10.0) pre-existing zarr files using NestedDirectoryStore are all zero when read.
                  
With an older version (tested with 2.3.0) the correct values are loaded.
                  
Creating a new zarr file using NestedDirectoryStore on 2.10.0 and reading it works correctly.
                  Version and installation information
                  Please provide the following:
                  • Value of zarr.__version__: '2.10.0'
                  • Value of numcodecs.__version__: '0.9.1'
                  • Version of Python interpreter: 3.8.11
                  • Operating system (Linux/Windows/Mac): Linux
                  • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip install
                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
                    No labels
                    No labels
                    Type
                    No type
                    Projects
                    No projects
                      Milestone
                      No milestone
                      Relationships
                      None yet
                      Development
                      No branches or pull requests
                      Issue actions
                      
, '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('^' + ".*" + '

                      Skip to content
                      zarr 2.10.0 fails to load pre-existing nested files #840
                      Closed
                      #850
                      Closed
                      zarr 2.10.0 fails to load pre-existing nested files#840
                      #850
                      Description
                      @abred
                      abred
                      opened on Sep 28, 2021
                      Minimal, reproducible code sample, a copy-pastable example if possible
                      importnumpyasnpimportzarra=np.ones((2,2)) z=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'w')
z['test'] =az=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'r')
print(np.array(z['test']))
arr=zarr.open(zarr.NestedDirectoryStore("path/to/existing/zarr/file.zarr"), 'r')
print(np.max(arr['volumes/raw']))
                      output with zarr 2.10.0:
                      
array([[1., 1.],
                      
[1., 1.]])
                      
0
                      output with zarr 2.3.0:
                      
array([[1., 1.],
                      
[1., 1.]])
                      
6733
                      Problem description
                      With the current version of zarr (2.10.0) pre-existing zarr files using NestedDirectoryStore are all zero when read.
                      
With an older version (tested with 2.3.0) the correct values are loaded.
                      
Creating a new zarr file using NestedDirectoryStore on 2.10.0 and reading it works correctly.
                      Version and installation information
                      Please provide the following:
                      • Value of zarr.__version__: '2.10.0'
                      • Value of numcodecs.__version__: '0.9.1'
                      • Version of Python interpreter: 3.8.11
                      • Operating system (Linux/Windows/Mac): Linux
                      • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip install
                      Metadata
                      Metadata
                      Assignees
                      No one assigned
                        Labels
                        No labels
                        No labels
                        Type
                        No type
                        Projects
                        No projects
                          Milestone
                          No milestone
                          Relationships
                          None yet
                          Development
                          No branches or pull requests
                          Issue actions
                          
, '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('^' + ".*" + '

                          Skip to content
                          zarr 2.10.0 fails to load pre-existing nested files #840
                          Closed
                          #850
                          Closed
                          zarr 2.10.0 fails to load pre-existing nested files#840
                          #850
                          Description
                          @abred
                          abred
                          opened on Sep 28, 2021
                          Minimal, reproducible code sample, a copy-pastable example if possible
                          importnumpyasnpimportzarra=np.ones((2,2)) z=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'w')
z['test'] =az=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'r')
print(np.array(z['test']))
arr=zarr.open(zarr.NestedDirectoryStore("path/to/existing/zarr/file.zarr"), 'r')
print(np.max(arr['volumes/raw']))
                          output with zarr 2.10.0:
                          
array([[1., 1.],
                          
[1., 1.]])
                          
0
                          output with zarr 2.3.0:
                          
array([[1., 1.],
                          
[1., 1.]])
                          
6733
                          Problem description
                          With the current version of zarr (2.10.0) pre-existing zarr files using NestedDirectoryStore are all zero when read.
                          
With an older version (tested with 2.3.0) the correct values are loaded.
                          
Creating a new zarr file using NestedDirectoryStore on 2.10.0 and reading it works correctly.
                          Version and installation information
                          Please provide the following:
                          • Value of zarr.__version__: '2.10.0'
                          • Value of numcodecs.__version__: '0.9.1'
                          • Version of Python interpreter: 3.8.11
                          • Operating system (Linux/Windows/Mac): Linux
                          • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip install
                          Metadata
                          Metadata
                          Assignees
                          No one assigned
                            Labels
                            No labels
                            No labels
                            Type
                            No type
                            Projects
                            No projects
                              Milestone
                              No milestone
                              Relationships
                              None yet
                              Development
                              No branches or pull requests
                              Issue actions
                              
, '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); }
})();
})();

                              Skip to content
                              zarr 2.10.0 fails to load pre-existing nested files #840
                              Closed
                              #850
                              Closed
                              zarr 2.10.0 fails to load pre-existing nested files#840
                              #850
                              Description
                              @abred
                              abred
                              opened on Sep 28, 2021
                              Minimal, reproducible code sample, a copy-pastable example if possible
                              importnumpyasnpimportzarra=np.ones((2,2)) z=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'w')
z['test'] =az=zarr.open(zarr.NestedDirectoryStore("test.zarr"), 'r')
print(np.array(z['test']))
arr=zarr.open(zarr.NestedDirectoryStore("path/to/existing/zarr/file.zarr"), 'r')
print(np.max(arr['volumes/raw']))
                              output with zarr 2.10.0:
                              
array([[1., 1.],
                              
[1., 1.]])
                              
0
                              output with zarr 2.3.0:
                              
array([[1., 1.],
                              
[1., 1.]])
                              
6733
                              Problem description
                              With the current version of zarr (2.10.0) pre-existing zarr files using NestedDirectoryStore are all zero when read.
                              
With an older version (tested with 2.3.0) the correct values are loaded.
                              
Creating a new zarr file using NestedDirectoryStore on 2.10.0 and reading it works correctly.
                              Version and installation information
                              Please provide the following:
                              • Value of zarr.__version__: '2.10.0'
                              • Value of numcodecs.__version__: '0.9.1'
                              • Version of Python interpreter: 3.8.11
                              • Operating system (Linux/Windows/Mac): Linux
                              • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip install
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