automatic backing of sdata.tables #498

Description

@ArneDefauw

I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail to get it working). This is how it used to work:


import anndata as ad
import numpy as np
import pandas as pd
from spatialdata import SpatialData
import spatialdata
import os
path=""
n_cells = 100
n_genes = 50
# Creating random data
X = np.random.randn(n_cells, n_genes)
obs = pd.DataFrame(index=[f'cell_{i}' for i in range(n_cells)])
var = pd.DataFrame(index=[f'gene_{i}' for i in range(n_genes)])
adata = ad.AnnData(X=X, obs=obs, var=var)
adata.obs['cell_type'] = ['type1' if i < n_cells // 2 else 'type2' for i in range(n_cells)]
adata.var['highly_variable'] = np.random.choice([True, False], size=n_genes)
sdata=SpatialData()
sdata.write( os.path.join( path, "sdata_dummy.zarr" ) )
sdata.tables[ "dummy_table" ] = spatialdata.models.TableModel.parse( adata,
)
assert sdata.table is not None # this is ok
sdata=SpatialData.read( os.path.join( path, "sdata_dummy.zarr" ) )
sdata
assert sdata.table is not None # this gives assertionerror

Is this related to #496?

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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

      automatic backing of sdata.tables #498

      Description

      @ArneDefauw

      I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail to get it working). This is how it used to work:

      
      import anndata as ad
      import numpy as np
      import pandas as pd
      from spatialdata import SpatialData
      import spatialdata
      import os
      path=""
      n_cells = 100
      n_genes = 50
      # Creating random data
      X = np.random.randn(n_cells, n_genes)
      obs = pd.DataFrame(index=[f'cell_{i}' for i in range(n_cells)])
      var = pd.DataFrame(index=[f'gene_{i}' for i in range(n_genes)])
      adata = ad.AnnData(X=X, obs=obs, var=var)
      adata.obs['cell_type'] = ['type1' if i < n_cells // 2 else 'type2' for i in range(n_cells)]
      adata.var['highly_variable'] = np.random.choice([True, False], size=n_genes)
      sdata=SpatialData()
      sdata.write( os.path.join( path, "sdata_dummy.zarr" ) )
      sdata.tables[ "dummy_table" ] = spatialdata.models.TableModel.parse( adata,
      )
      assert sdata.table is not None # this is ok
      sdata=SpatialData.read( os.path.join( path, "sdata_dummy.zarr" ) )
      sdata
      assert sdata.table is not None # this gives assertionerror
      

      Is this related to #496?

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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

          automatic backing of sdata.tables #498

          Description

          @ArneDefauw

          I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail to get it working). This is how it used to work:

          
          import anndata as ad
          import numpy as np
          import pandas as pd
          from spatialdata import SpatialData
          import spatialdata
          import os
          path=""
          n_cells = 100
          n_genes = 50
          # Creating random data
          X = np.random.randn(n_cells, n_genes)
          obs = pd.DataFrame(index=[f'cell_{i}' for i in range(n_cells)])
          var = pd.DataFrame(index=[f'gene_{i}' for i in range(n_genes)])
          adata = ad.AnnData(X=X, obs=obs, var=var)
          adata.obs['cell_type'] = ['type1' if i < n_cells // 2 else 'type2' for i in range(n_cells)]
          adata.var['highly_variable'] = np.random.choice([True, False], size=n_genes)
          sdata=SpatialData()
          sdata.write( os.path.join( path, "sdata_dummy.zarr" ) )
          sdata.tables[ "dummy_table" ] = spatialdata.models.TableModel.parse( adata,
          )
          assert sdata.table is not None # this is ok
          sdata=SpatialData.read( os.path.join( path, "sdata_dummy.zarr" ) )
          sdata
          assert sdata.table is not None # this gives assertionerror
          

          Is this related to #496?

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              , '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

              automatic backing of sdata.tables #498

              Description

              @ArneDefauw

              I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail to get it working). This is how it used to work:

              
              import anndata as ad
              import numpy as np
              import pandas as pd
              from spatialdata import SpatialData
              import spatialdata
              import os
              path=""
              n_cells = 100
              n_genes = 50
              # Creating random data
              X = np.random.randn(n_cells, n_genes)
              obs = pd.DataFrame(index=[f'cell_{i}' for i in range(n_cells)])
              var = pd.DataFrame(index=[f'gene_{i}' for i in range(n_genes)])
              adata = ad.AnnData(X=X, obs=obs, var=var)
              adata.obs['cell_type'] = ['type1' if i < n_cells // 2 else 'type2' for i in range(n_cells)]
              adata.var['highly_variable'] = np.random.choice([True, False], size=n_genes)
              sdata=SpatialData()
              sdata.write( os.path.join( path, "sdata_dummy.zarr" ) )
              sdata.tables[ "dummy_table" ] = spatialdata.models.TableModel.parse( adata,
              )
              assert sdata.table is not None # this is ok
              sdata=SpatialData.read( os.path.join( path, "sdata_dummy.zarr" ) )
              sdata
              assert sdata.table is not None # this gives assertionerror
              

              Is this related to #496?

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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

                  automatic backing of sdata.tables #498

                  Description

                  @ArneDefauw

                  I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail to get it working). This is how it used to work:

                  
                  import anndata as ad
                  import numpy as np
                  import pandas as pd
                  from spatialdata import SpatialData
                  import spatialdata
                  import os
                  path=""
                  n_cells = 100
                  n_genes = 50
                  # Creating random data
                  X = np.random.randn(n_cells, n_genes)
                  obs = pd.DataFrame(index=[f'cell_{i}' for i in range(n_cells)])
                  var = pd.DataFrame(index=[f'gene_{i}' for i in range(n_genes)])
                  adata = ad.AnnData(X=X, obs=obs, var=var)
                  adata.obs['cell_type'] = ['type1' if i < n_cells // 2 else 'type2' for i in range(n_cells)]
                  adata.var['highly_variable'] = np.random.choice([True, False], size=n_genes)
                  sdata=SpatialData()
                  sdata.write( os.path.join( path, "sdata_dummy.zarr" ) )
                  sdata.tables[ "dummy_table" ] = spatialdata.models.TableModel.parse( adata,
                  )
                  assert sdata.table is not None # this is ok
                  sdata=SpatialData.read( os.path.join( path, "sdata_dummy.zarr" ) )
                  sdata
                  assert sdata.table is not None # this gives assertionerror
                  

                  Is this related to #496?

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                      , '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

                      automatic backing of sdata.tables #498

                      Description

                      @ArneDefauw

                      I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail to get it working). This is how it used to work:

                      
                      import anndata as ad
                      import numpy as np
                      import pandas as pd
                      from spatialdata import SpatialData
                      import spatialdata
                      import os
                      path=""
                      n_cells = 100
                      n_genes = 50
                      # Creating random data
                      X = np.random.randn(n_cells, n_genes)
                      obs = pd.DataFrame(index=[f'cell_{i}' for i in range(n_cells)])
                      var = pd.DataFrame(index=[f'gene_{i}' for i in range(n_genes)])
                      adata = ad.AnnData(X=X, obs=obs, var=var)
                      adata.obs['cell_type'] = ['type1' if i < n_cells // 2 else 'type2' for i in range(n_cells)]
                      adata.var['highly_variable'] = np.random.choice([True, False], size=n_genes)
                      sdata=SpatialData()
                      sdata.write( os.path.join( path, "sdata_dummy.zarr" ) )
                      sdata.tables[ "dummy_table" ] = spatialdata.models.TableModel.parse( adata,
                      )
                      assert sdata.table is not None # this is ok
                      sdata=SpatialData.read( os.path.join( path, "sdata_dummy.zarr" ) )
                      sdata
                      assert sdata.table is not None # this gives assertionerror
                      

                      Is this related to #496?

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                          , '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

                          automatic backing of sdata.tables #498

                          Description

                          @ArneDefauw

                          I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail to get it working). This is how it used to work:

                          
                          import anndata as ad
                          import numpy as np
                          import pandas as pd
                          from spatialdata import SpatialData
                          import spatialdata
                          import os
                          path=""
                          n_cells = 100
                          n_genes = 50
                          # Creating random data
                          X = np.random.randn(n_cells, n_genes)
                          obs = pd.DataFrame(index=[f'cell_{i}' for i in range(n_cells)])
                          var = pd.DataFrame(index=[f'gene_{i}' for i in range(n_genes)])
                          adata = ad.AnnData(X=X, obs=obs, var=var)
                          adata.obs['cell_type'] = ['type1' if i < n_cells // 2 else 'type2' for i in range(n_cells)]
                          adata.var['highly_variable'] = np.random.choice([True, False], size=n_genes)
                          sdata=SpatialData()
                          sdata.write( os.path.join( path, "sdata_dummy.zarr" ) )
                          sdata.tables[ "dummy_table" ] = spatialdata.models.TableModel.parse( adata,
                          )
                          assert sdata.table is not None # this is ok
                          sdata=SpatialData.read( os.path.join( path, "sdata_dummy.zarr" ) )
                          sdata
                          assert sdata.table is not None # this gives assertionerror
                          

                          Is this related to #496?

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                              , '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

                              automatic backing of sdata.tables #498

                              Description

                              @ArneDefauw

                              I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail to get it working). This is how it used to work:

                              
                              import anndata as ad
                              import numpy as np
                              import pandas as pd
                              from spatialdata import SpatialData
                              import spatialdata
                              import os
                              path=""
                              n_cells = 100
                              n_genes = 50
                              # Creating random data
                              X = np.random.randn(n_cells, n_genes)
                              obs = pd.DataFrame(index=[f'cell_{i}' for i in range(n_cells)])
                              var = pd.DataFrame(index=[f'gene_{i}' for i in range(n_genes)])
                              adata = ad.AnnData(X=X, obs=obs, var=var)
                              adata.obs['cell_type'] = ['type1' if i < n_cells // 2 else 'type2' for i in range(n_cells)]
                              adata.var['highly_variable'] = np.random.choice([True, False], size=n_genes)
                              sdata=SpatialData()
                              sdata.write( os.path.join( path, "sdata_dummy.zarr" ) )
                              sdata.tables[ "dummy_table" ] = spatialdata.models.TableModel.parse( adata,
                              )
                              assert sdata.table is not None # this is ok
                              sdata=SpatialData.read( os.path.join( path, "sdata_dummy.zarr" ) )
                              sdata
                              assert sdata.table is not None # this gives assertionerror
                              

                              Is this related to #496?

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