zarr.open and friends should handle Path objects #601

Closed
Closed
zarr.open and friends should handle Path objects#601

Description

@clbarnes
clbarnes
opened on Sep 11, 2020

Strictly, anything which doesn't cause os.fspath to raise a TypeError.

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

importzarrfrompathlibimportPathpath_str="path/to/array.zarr"zarr.open(path_str) # works finezarr.open(Path(path_str)) # fails with TypeError because it's not a str and not iterable

Problem description

pathlib is great and everyone should use it whenever appropriate. Personally, I even subclass PurePosixPath for manipulations of object names inside hdf5/ zarr/ n5 containers.

People with zarr objects on the file system should want to use Paths to refer to them, so zarr should support people doing so.

This should just be a case of trying os.fspath on the store/path argument(s) for most of the functions in convenience.

Version and installation information

Please provide the following:

  • Value of zarr.__version__: 2.4.0
  • Value of numcodecs.__version__: 0.6.4
  • Version of Python interpreter: 3.8.5
  • Operating system (Linux/Windows/Mac): Linux
  • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip in virtual environment

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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.open and friends should handle Path objects #601
      Closed
      Closed
      zarr.open and friends should handle Path objects#601
      Description
      @clbarnes
      clbarnes
      opened on Sep 11, 2020
      Strictly, anything which doesn't cause os.fspath to raise a TypeError.
      Minimal, reproducible code sample, a copy-pastable example if possible
      importzarrfrompathlibimportPathpath_str="path/to/array.zarr"zarr.open(path_str) # works finezarr.open(Path(path_str)) # fails with TypeError because it's not a str and not iterable
      Problem description
      pathlib is great and everyone should use it whenever appropriate. Personally, I even subclass PurePosixPath for manipulations of object names inside hdf5/ zarr/ n5 containers.
      People with zarr objects on the file system should want to use Paths to refer to them, so zarr should support people doing so.
      This should just be a case of trying os.fspath on the store/path argument(s) for most of the functions in convenience.
      Version and installation information
      Please provide the following:
      • Value of zarr.__version__: 2.4.0
      • Value of numcodecs.__version__: 0.6.4
      • Version of Python interpreter: 3.8.5
      • Operating system (Linux/Windows/Mac): Linux
      • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip in virtual environment
      Metadata
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, '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.open and friends should handle Path objects #601
          Closed
          Closed
          zarr.open and friends should handle Path objects#601
          Description
          @clbarnes
          clbarnes
          opened on Sep 11, 2020
          Strictly, anything which doesn't cause os.fspath to raise a TypeError.
          Minimal, reproducible code sample, a copy-pastable example if possible
          importzarrfrompathlibimportPathpath_str="path/to/array.zarr"zarr.open(path_str) # works finezarr.open(Path(path_str)) # fails with TypeError because it's not a str and not iterable
          Problem description
          pathlib is great and everyone should use it whenever appropriate. Personally, I even subclass PurePosixPath for manipulations of object names inside hdf5/ zarr/ n5 containers.
          People with zarr objects on the file system should want to use Paths to refer to them, so zarr should support people doing so.
          This should just be a case of trying os.fspath on the store/path argument(s) for most of the functions in convenience.
          Version and installation information
          Please provide the following:
          • Value of zarr.__version__: 2.4.0
          • Value of numcodecs.__version__: 0.6.4
          • Version of Python interpreter: 3.8.5
          • Operating system (Linux/Windows/Mac): Linux
          • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip in virtual environment
          Metadata
          Metadata
          Assignees
          No one assigned
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            No labels
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              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.open and friends should handle Path objects #601
              Closed
              Closed
              zarr.open and friends should handle Path objects#601
              Description
              @clbarnes
              clbarnes
              opened on Sep 11, 2020
              Strictly, anything which doesn't cause os.fspath to raise a TypeError.
              Minimal, reproducible code sample, a copy-pastable example if possible
              importzarrfrompathlibimportPathpath_str="path/to/array.zarr"zarr.open(path_str) # works finezarr.open(Path(path_str)) # fails with TypeError because it's not a str and not iterable
              Problem description
              pathlib is great and everyone should use it whenever appropriate. Personally, I even subclass PurePosixPath for manipulations of object names inside hdf5/ zarr/ n5 containers.
              People with zarr objects on the file system should want to use Paths to refer to them, so zarr should support people doing so.
              This should just be a case of trying os.fspath on the store/path argument(s) for most of the functions in convenience.
              Version and installation information
              Please provide the following:
              • Value of zarr.__version__: 2.4.0
              • Value of numcodecs.__version__: 0.6.4
              • Version of Python interpreter: 3.8.5
              • Operating system (Linux/Windows/Mac): Linux
              • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip in virtual environment
              Metadata
              Metadata
              Assignees
              No one assigned
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                No labels
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, '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.open and friends should handle Path objects #601
                  Closed
                  Closed
                  zarr.open and friends should handle Path objects#601
                  Description
                  @clbarnes
                  clbarnes
                  opened on Sep 11, 2020
                  Strictly, anything which doesn't cause os.fspath to raise a TypeError.
                  Minimal, reproducible code sample, a copy-pastable example if possible
                  importzarrfrompathlibimportPathpath_str="path/to/array.zarr"zarr.open(path_str) # works finezarr.open(Path(path_str)) # fails with TypeError because it's not a str and not iterable
                  Problem description
                  pathlib is great and everyone should use it whenever appropriate. Personally, I even subclass PurePosixPath for manipulations of object names inside hdf5/ zarr/ n5 containers.
                  People with zarr objects on the file system should want to use Paths to refer to them, so zarr should support people doing so.
                  This should just be a case of trying os.fspath on the store/path argument(s) for most of the functions in convenience.
                  Version and installation information
                  Please provide the following:
                  • Value of zarr.__version__: 2.4.0
                  • Value of numcodecs.__version__: 0.6.4
                  • Version of Python interpreter: 3.8.5
                  • Operating system (Linux/Windows/Mac): Linux
                  • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip in virtual environment
                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
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                    No labels
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                    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.open and friends should handle Path objects #601
                      Closed
                      Closed
                      zarr.open and friends should handle Path objects#601
                      Description
                      @clbarnes
                      clbarnes
                      opened on Sep 11, 2020
                      Strictly, anything which doesn't cause os.fspath to raise a TypeError.
                      Minimal, reproducible code sample, a copy-pastable example if possible
                      importzarrfrompathlibimportPathpath_str="path/to/array.zarr"zarr.open(path_str) # works finezarr.open(Path(path_str)) # fails with TypeError because it's not a str and not iterable
                      Problem description
                      pathlib is great and everyone should use it whenever appropriate. Personally, I even subclass PurePosixPath for manipulations of object names inside hdf5/ zarr/ n5 containers.
                      People with zarr objects on the file system should want to use Paths to refer to them, so zarr should support people doing so.
                      This should just be a case of trying os.fspath on the store/path argument(s) for most of the functions in convenience.
                      Version and installation information
                      Please provide the following:
                      • Value of zarr.__version__: 2.4.0
                      • Value of numcodecs.__version__: 0.6.4
                      • Version of Python interpreter: 3.8.5
                      • Operating system (Linux/Windows/Mac): Linux
                      • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip in virtual environment
                      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.open and friends should handle Path objects #601
                          Closed
                          Closed
                          zarr.open and friends should handle Path objects#601
                          Description
                          @clbarnes
                          clbarnes
                          opened on Sep 11, 2020
                          Strictly, anything which doesn't cause os.fspath to raise a TypeError.
                          Minimal, reproducible code sample, a copy-pastable example if possible
                          importzarrfrompathlibimportPathpath_str="path/to/array.zarr"zarr.open(path_str) # works finezarr.open(Path(path_str)) # fails with TypeError because it's not a str and not iterable
                          Problem description
                          pathlib is great and everyone should use it whenever appropriate. Personally, I even subclass PurePosixPath for manipulations of object names inside hdf5/ zarr/ n5 containers.
                          People with zarr objects on the file system should want to use Paths to refer to them, so zarr should support people doing so.
                          This should just be a case of trying os.fspath on the store/path argument(s) for most of the functions in convenience.
                          Version and installation information
                          Please provide the following:
                          • Value of zarr.__version__: 2.4.0
                          • Value of numcodecs.__version__: 0.6.4
                          • Version of Python interpreter: 3.8.5
                          • Operating system (Linux/Windows/Mac): Linux
                          • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip in virtual environment
                          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.open and friends should handle Path objects #601
                              Closed
                              Closed
                              zarr.open and friends should handle Path objects#601
                              Description
                              @clbarnes
                              clbarnes
                              opened on Sep 11, 2020
                              Strictly, anything which doesn't cause os.fspath to raise a TypeError.
                              Minimal, reproducible code sample, a copy-pastable example if possible
                              importzarrfrompathlibimportPathpath_str="path/to/array.zarr"zarr.open(path_str) # works finezarr.open(Path(path_str)) # fails with TypeError because it's not a str and not iterable
                              Problem description
                              pathlib is great and everyone should use it whenever appropriate. Personally, I even subclass PurePosixPath for manipulations of object names inside hdf5/ zarr/ n5 containers.
                              People with zarr objects on the file system should want to use Paths to refer to them, so zarr should support people doing so.
                              This should just be a case of trying os.fspath on the store/path argument(s) for most of the functions in convenience.
                              Version and installation information
                              Please provide the following:
                              • Value of zarr.__version__: 2.4.0
                              • Value of numcodecs.__version__: 0.6.4
                              • Version of Python interpreter: 3.8.5
                              • Operating system (Linux/Windows/Mac): Linux
                              • How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): pip in virtual environment
                              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