v1.26.0.dev202611130643

Nightly build of PyReconstruct Dev from main at f58ef18.

What's Changed

• docs(store): correct trace-store repair sites and readers by @dustenhubbard in #1236
• fix(installers): finish all-users installation by @dustenhubbard in #1227
• fix: preserve existing scaled image destinations by @dustenhubbard in #1206
• test(field): cover drawing and selection gestures by @dustenhubbard in #1191
• ci(nightly): schedule earlier and replace retiring macOS runners by @dustenhubbard in #1123
• fix(align): mask section flaws and refuse weak correlation matches by @dustenhubbard in #1132
• test: keep series option writes in a per-test store by @dustenhubbard in #1239
• fix: open 3D settings from the scene and rebuild changed meshes by @dustenhubbard in #1131
• fix: refresh and preserve quantitative measurements by @dustenhubbard in #1214
• fix(packaging): keep PyReconstruct sealed in the dmg on macOS by @dustenhubbard in #1241
• test(store): keep the Linux mount table tests off host links by @dustenhubbard in #1245
• fix(options): leave room for the real scrollbar width by @dustenhubbard in #1246
• test: delete the top-level widgets a test leaves behind by @dustenhubbard in #1240
• test(3d): keep a selected mesh that cannot regenerate on reload by @dustenhubbard in #1247
• test(store): pin the clock for the store-open save comparison by @dustenhubbard in #1248
• fix(mouse): ignore held presses after tool changes by @dustenhubbard in #1130
• feat(palette): choose trace row length and tool columns by @dustenhubbard in #1225
• test(measurements): compare real traces with pinned upstream values by @dustenhubbard in #1249
• fix(mouse): end line tracing when a tool replaces a pending z-trace by @dustenhubbard in #1250
• fix(settings): migrate KHLab preferences to PyReconstruct by @dustenhubbard in #1143

Full Changelog: v1.26.0.dev202611120955...v1.26.0.dev202611130643

v1.26.0.dev202611050936

Nightly build of PyReconstruct Dev from main at 68a5a97.

Changes since v1.25.0

Added

• Open a series from a terminal with pyrecon file.jser or pyreconstruct file.jser. PyReconstruct Dev answers to pyrecon-dev.
• PyReconstruct Dev on macOS installs an update when you quit and reopens a few seconds later. If it cannot, the update uses the disk image as before.
• PyReconstruct Dev on Windows can install an update when you quit, without the installer. It turns on in a later Dev release; until then, updates use the installer as before.
• Help ▸ Online resources ▸ Class documents opens the class pages on pyreconstruct.org. In macOS Dev builds it is also Help ▸ Class documents.

Changed

• Security fixes for reading and writing image files, including JPEG, TIFF, PNG, GIF, PDF and EPS. Exporting a section as SVG or PNG works as before.
• Help ▸ PyReconstruct user guide now opens the guide on pyreconstruct.org. The older GitHub wiki pages stay online.
• Opening a series while another is open needs less memory. A load that fails or is canceled after the file is chosen leaves no series open.
• Traces draw faster on dense sections, most of all with the whole section in view. Paging and zooming show the same picture as before.
• The name under the mouse keeps up on dense sections zoomed out. It shows the same trace as before, and paging is a little faster.
• Large series open faster. A series with half a million traces opens in about a third of the time, with the same objects and numbers as before.
• Paging through a large series no longer stalls every few sections. The pause of about a second that came every 4 to 10 section changes on a series with half a million traces is gone, and memory use is the same as before.
• Changing sections in a large series is faster. A section with half a million points opens about 0.15 s sooner, and PyReconstruct uses a little less memory while paging.
• Paging through the sections of a large series is faster. Stepping to the next or previous section waits less after an edit and with the whole section in view, and less for the image to open on a series with image files.

Fixed

• Status bar names with stacked accents, such as Ẫ, no longer lose their top. The alignment and brightness/contrast pills make room for the accent.
• Opening another series no longer keeps the last one in memory after a clean-up list was shown. Pixel dust, Duplicates, the self-crossing lists and the smoothing list let go of the series they named.
• A slow click in Combo trace mode starts a point-by-point trace. A click held longer than a moment, with a pixel or two of drift, no longer draws nothing.
• Opening another series frees the memory of the one that was open. The first series opened in a session stayed in memory until PyReconstruct quit, so a second open of a large series could double its memory use.
• An open asked for while another open runs is now skipped with a notice. The skipped series no longer leaves its working folder on disk.
• Changing sections while a series opens no longer shows a file error.
• Canceling the Open Series file dialog keeps your unsaved edits. The file dialog now comes before the save prompt, so backing out of it leaves the open series exactly as it was.
• A NUL character in the series code or a backup name now gives a clear notice. Save and close still finish, and Series ▸ Series code ▸ Set series code and File ▸ Backup ▸ Settings refuse the character.
• A close that is blocked or interrupted never leaves a series with sections missing. A backup folder inside the series' hidden working folder is no longer accepted, since a close deletes that folder.
• When a save or close fails, the window and the series stay open. Free space or close the program using the file, then save or close again.
• CSV, XML and crop log exports no longer stop on a name with a broken character. Old or damaged files can hold such a name, and the export now writes the character as text.
• Opening a series from the Finder no longer redirects or loses work. While a dialog or progress window is open, including at startup, or a series is opening, importing, saving or closing, PyReconstruct skips the open and says so.
• A series opens again after you edit an object with a broken character in its name. Old or damaged files can hold such a name, and it now stays the same through Save and reopen.
• The tool buttons no longer hide under the sliders in a short window. The brightness and contrast sliders and the section buttons move left of the tool column when it reaches down to them, so every button can be clicked.
• Save As now reports failures to move, rename or write the series. The notice says where the series and its working files are.
• On Linux, a series whose code holds a NUL character no longer freezes PyReconstruct. Its own settings, such as backups, now load and save.
• Opening a series with no series code no longer marks it as edited. Changing sections then saves nothing until you edit something.
• On Linux and Windows, a series code can no longer reach another series' settings. A code with a doubled slash or backslash, a trailing backslash, or a "." or ".." part has settings of its own.
• On Linux with Noto Sans, code in What's New matches the size of the text around it.
• The progress window closes when a legacy series import finishes or fails.

---

What's Changed

• chore(deps): bump tornado from 6.5.10 to 6.6 by @dependabot[bot] in #1229
• chore(deps): bump pyasn1 from 0.6.4 to 0.6.5 by @dependabot[bot] in #1230

Full Changelog: v1.26.0.dev202611030940...v1.26.0.dev202611050936

v1.26.0.dev202611030940

Nightly build of PyReconstruct Dev from main at 46e5722.

Changes since v1.25.0

Added

• Open a series from a terminal with pyrecon file.jser or pyreconstruct file.jser. PyReconstruct Dev answers to pyrecon-dev.
• PyReconstruct Dev on macOS installs an update when you quit and reopens a few seconds later. If it cannot, the update uses the disk image as before.
• PyReconstruct Dev on Windows can install an update when you quit, without the installer. It turns on in a later Dev release; until then, updates use the installer as before.
• Help ▸ Online resources ▸ Class documents opens the class pages on pyreconstruct.org. In macOS Dev builds it is also Help ▸ Class documents.

Changed

• Security fixes for reading and writing image files, including JPEG, TIFF, PNG, GIF, PDF and EPS. Exporting a section as SVG or PNG works as before.
• Help ▸ PyReconstruct user guide now opens the guide on pyreconstruct.org. The older GitHub wiki pages stay online.
• Opening a series while another is open needs less memory. A load that fails or is canceled after the file is chosen leaves no series open.
• Traces draw faster on dense sections, most of all with the whole section in view. Paging and zooming show the same picture as before.
• The name under the mouse keeps up on dense sections zoomed out. It shows the same trace as before, and paging is a little faster.
• Large series open faster. A series with half a million traces opens in about a third of the time, with the same objects and numbers as before.
• Paging through a large series no longer stalls every few sections. The pause of about a second that came every 4 to 10 section changes on a series with half a million traces is gone, and memory use is the same as before.
• Changing sections in a large series is faster. A section with half a million points opens about 0.15 s sooner, and PyReconstruct uses a little less memory while paging.
• Paging through the sections of a large series is faster. Stepping to the next or previous section waits less after an edit and with the whole section in view, and less for the image to open on a series with image files.

Fixed

• Status bar names with stacked accents, such as Ẫ, no longer lose their top. The alignment and brightness/contrast pills make room for the accent.
• Opening another series no longer keeps the last one in memory after a clean-up list was shown. Pixel dust, Duplicates, the self-crossing lists and the smoothing list let go of the series they named.
• A slow click in Combo trace mode starts a point-by-point trace. A click held longer than a moment, with a pixel or two of drift, no longer draws nothing.
• Opening another series frees the memory of the one that was open. The first series opened in a session stayed in memory until PyReconstruct quit, so a second open of a large series could double its memory use.
• An open asked for while another open runs is now skipped with a notice. The skipped series no longer leaves its working folder on disk.
• Changing sections while a series opens no longer shows a file error.
• Canceling the Open Series file dialog keeps your unsaved edits. The file dialog now comes before the save prompt, so backing out of it leaves the open series exactly as it was.
• A NUL character in the series code or a backup name now gives a clear notice. Save and close still finish, and Series ▸ Series code ▸ Set series code and File ▸ Backup ▸ Settings refuse the character.
• A close that is blocked or interrupted never leaves a series with sections missing. A backup folder inside the series' hidden working folder is no longer accepted, since a close deletes that folder.
• When a save or close fails, the window and the series stay open. Free space or close the program using the file, then save or close again.
• CSV, XML and crop log exports no longer stop on a name with a broken character. Old or damaged files can hold such a name, and the export now writes the character as text.
• Opening a series from the Finder no longer redirects or loses work. While a dialog or progress window is open, including at startup, or a series is opening, importing, saving or closing, PyReconstruct skips the open and says so.
• A series opens again after you edit an object with a broken character in its name. Old or damaged files can hold such a name, and it now stays the same through Save and reopen.
• The tool buttons no longer hide under the sliders in a short window. The brightness and contrast sliders and the section buttons move left of the tool column when it reaches down to them, so every button can be clicked.
• Save As now reports failures to move, rename or write the series. The notice says where the series and its working files are.
• On Linux, a series whose code holds a NUL character no longer freezes PyReconstruct. Its own settings, such as backups, now load and save.
• Opening a series with no series code no longer marks it as edited. Changing sections then saves nothing until you edit something.
• On Linux and Windows, a series code can no longer reach another series' settings. A code with a doubled slash or backslash, a trailing backslash, or a "." or ".." part has settings of its own.
• On Linux with Noto Sans, code in What's New matches the size of the text around it.
• The progress window closes when a legacy series import finishes or fails.

---

What's Changed

• test(ztrace): compare points one at a time by @dustenhubbard in #1203
• feat(roi): let the ROI box follow an object through the series by @dustenhubbard in #1139
• feat(roi): show whole every object that touches the ROI box by @dustenhubbard in #1220

Full Changelog: v1.26.0.dev202611020937...v1.26.0.dev202611030940

v1.26.0.dev202611020937

Nightly build of PyReconstruct Dev from main at d3c4737.

Changes since v1.25.0

Added

• Open a series from a terminal with pyrecon file.jser or pyreconstruct file.jser. PyReconstruct Dev answers to pyrecon-dev.
• PyReconstruct Dev on macOS installs an update when you quit and reopens a few seconds later. If it cannot, the update uses the disk image as before.
• PyReconstruct Dev on Windows can install an update when you quit, without the installer. It turns on in a later Dev release; until then, updates use the installer as before.
• Help ▸ Online resources ▸ Class documents opens the class pages on pyreconstruct.org. In macOS Dev builds it is also Help ▸ Class documents.

Changed

• Security fixes for reading and writing image files, including JPEG, TIFF, PNG, GIF, PDF and EPS. Exporting a section as SVG or PNG works as before.
• Help ▸ PyReconstruct user guide now opens the guide on pyreconstruct.org. The older GitHub wiki pages stay online.
• Opening a series while another is open needs less memory. A load that fails or is canceled after the file is chosen leaves no series open.
• Traces draw faster on dense sections, most of all with the whole section in view. Paging and zooming show the same picture as before.
• The name under the mouse keeps up on dense sections zoomed out. It shows the same trace as before, and paging is a little faster.
• Large series open faster. A series with half a million traces opens in about a third of the time, with the same objects and numbers as before.
• Paging through a large series no longer stalls every few sections. The pause of about a second that came every 4 to 10 section changes on a series with half a million traces is gone, and memory use is the same as before.
• Changing sections in a large series is faster. A section with half a million points opens about 0.15 s sooner, and PyReconstruct uses a little less memory while paging.
• Paging through the sections of a large series is faster. Stepping to the next or previous section waits less after an edit and with the whole section in view, and less for the image to open on a series with image files.

Fixed

• Status bar names with stacked accents, such as Ẫ, no longer lose their top. The alignment and brightness/contrast pills make room for the accent.
• Opening another series no longer keeps the last one in memory after a clean-up list was shown. Pixel dust, Duplicates, the self-crossing lists and the smoothing list let go of the series they named.
• A slow click in Combo trace mode starts a point-by-point trace. A click held longer than a moment, with a pixel or two of drift, no longer draws nothing.
• Opening another series frees the memory of the one that was open. The first series opened in a session stayed in memory until PyReconstruct quit, so a second open of a large series could double its memory use.
• An open asked for while another open runs is now skipped with a notice. The skipped series no longer leaves its working folder on disk.
• Changing sections while a series opens no longer shows a file error.
• Canceling the Open Series file dialog keeps your unsaved edits. The file dialog now comes before the save prompt, so backing out of it leaves the open series exactly as it was.
• A NUL character in the series code or a backup name now gives a clear notice. Save and close still finish, and Series ▸ Series code ▸ Set series code and File ▸ Backup ▸ Settings refuse the character.
• A close that is blocked or interrupted never leaves a series with sections missing. A backup folder inside the series' hidden working folder is no longer accepted, since a close deletes that folder.
• When a save or close fails, the window and the series stay open. Free space or close the program using the file, then save or close again.
• CSV, XML and crop log exports no longer stop on a name with a broken character. Old or damaged files can hold such a name, and the export now writes the character as text.
• Opening a series from the Finder no longer redirects or loses work. While a dialog or progress window is open, including at startup, or a series is opening, importing, saving or closing, PyReconstruct skips the open and says so.
• A series opens again after you edit an object with a broken character in its name. Old or damaged files can hold such a name, and it now stays the same through Save and reopen.
• The tool buttons no longer hide under the sliders in a short window. The brightness and contrast sliders and the section buttons move left of the tool column when it reaches down to them, so every button can be clicked.
• Save As now reports failures to move, rename or write the series. The notice says where the series and its working files are.
• On Linux, a series whose code holds a NUL character no longer freezes PyReconstruct. Its own settings, such as backups, now load and save.
• Opening a series with no series code no longer marks it as edited. Changing sections then saves nothing until you edit something.
• On Linux and Windows, a series code can no longer reach another series' settings. A code with a doubled slash or backslash, a trailing backslash, or a "." or ".." part has settings of its own.
• On Linux with Noto Sans, code in What's New matches the size of the text around it.
• The progress window closes when a legacy series import finishes or fails.

---

What's Changed

• feat(roi): set how the ROI tool places the box, and drop B by @dustenhubbard in #1118
• perf(load): build a trace's points from the file's lists on first read by @dustenhubbard in #1122

Full Changelog: v1.26.0.dev202610310829...v1.26.0.dev202611020937

v1.26.0.dev202610310829

Nightly build of PyReconstruct Dev from main at a97b582.

Changes since v1.25.0

Added

• Open a series from a terminal with pyrecon file.jser or pyreconstruct file.jser. PyReconstruct Dev answers to pyrecon-dev.
• PyReconstruct Dev on macOS installs an update when you quit and reopens a few seconds later. If it cannot, the update uses the disk image as before.
• PyReconstruct Dev on Windows can install an update when you quit, without the installer. It turns on in a later Dev release; until then, updates use the installer as before.
• Help ▸ Online resources ▸ Class documents opens the class pages on pyreconstruct.org. In macOS Dev builds it is also Help ▸ Class documents.

Changed

• Security fixes for reading and writing image files, including JPEG, TIFF, PNG, GIF, PDF and EPS. Exporting a section as SVG or PNG works as before.
• Help ▸ PyReconstruct user guide now opens the guide on pyreconstruct.org. The older GitHub wiki pages stay online.
• Opening a series while another is open needs less memory. A load that fails or is canceled after the file is chosen leaves no series open.
• Traces draw faster on dense sections, most of all with the whole section in view. Paging and zooming show the same picture as before.
• The name under the mouse keeps up on dense sections zoomed out. It shows the same trace as before, and paging is a little faster.
• Large series open faster. A series with half a million traces opens in about a third of the time, with the same objects and numbers as before.
• Paging through a large series no longer stalls every few sections. The pause of about a second that came every 4 to 10 section changes on a series with half a million traces is gone, and memory use is the same as before.
• Paging through the sections of a large series is faster. Stepping to the next or previous section waits less after an edit and with the whole section in view, and less for the image to open on a series with image files.

Fixed

• Status bar names with stacked accents, such as Ẫ, no longer lose their top. The alignment and brightness/contrast pills make room for the accent.
• Opening another series no longer keeps the last one in memory after a clean-up list was shown. Pixel dust, Duplicates, the self-crossing lists and the smoothing list let go of the series they named.
• A slow click in Combo trace mode starts a point-by-point trace. A click held longer than a moment, with a pixel or two of drift, no longer draws nothing.
• Opening another series frees the memory of the one that was open. The first series opened in a session stayed in memory until PyReconstruct quit, so a second open of a large series could double its memory use.
• An open asked for while another open runs is now skipped with a notice. The skipped series no longer leaves its working folder on disk.
• Changing sections while a series opens no longer shows a file error.
• Canceling the Open Series file dialog keeps your unsaved edits. The file dialog now comes before the save prompt, so backing out of it leaves the open series exactly as it was.
• A NUL character in the series code or a backup name now gives a clear notice. Save and close still finish, and Series ▸ Series code ▸ Set series code and File ▸ Backup ▸ Settings refuse the character.
• A close that is blocked or interrupted never leaves a series with sections missing. A backup folder inside the series' hidden working folder is no longer accepted, since a close deletes that folder.
• When a save or close fails, the window and the series stay open. Free space or close the program using the file, then save or close again.
• CSV, XML and crop log exports no longer stop on a name with a broken character. Old or damaged files can hold such a name, and the export now writes the character as text.
• Opening a series from the Finder no longer redirects or loses work. While a dialog or progress window is open, including at startup, or a series is opening, importing, saving or closing, PyReconstruct skips the open and says so.
• A series opens again after you edit an object with a broken character in its name. Old or damaged files can hold such a name, and it now stays the same through Save and reopen.
• The tool buttons no longer hide under the sliders in a short window. The brightness and contrast sliders and the section buttons move left of the tool column when it reaches down to them, so every button can be clicked.
• Save As now reports failures to move, rename or write the series. The notice says where the series and its working files are.
• On Linux, a series whose code holds a NUL character no longer freezes PyReconstruct. Its own settings, such as backups, now load and save.
• Opening a series with no series code no longer marks it as edited. Changing sections then saves nothing until you edit something.
• On Linux and Windows, a series code can no longer reach another series' settings. A code with a doubled slash or backslash, a trailing backslash, or a "." or ".." part has settings of its own.
• On Linux with Noto Sans, code in What's New matches the size of the text around it.
• The progress window closes when a legacy series import finishes or fails.

---

What's Changed

• perf(open): free the open series before a new one loads by @dustenhubbard in #1111
• fix(open): keep unsaved edits when the file picker is canceled by @dustenhubbard in #1113
• fix(open): release cleanup lists when a series closes by @dustenhubbard in #1114
• test(save): give the save prompt tests a QApplication by @dustenhubbard in #1117
• fix(open): free an old series that outlives the next open by @dustenhubbard in #1116

Full Changelog: v1.26.0.dev202610300844...v1.26.0.dev202610310829

v1.26.0.dev202610300844

Nightly build of PyReconstruct Dev from main at b4c6cf8.

Changes since v1.25.0

Added

• Open a series from a terminal with pyrecon file.jser or pyreconstruct file.jser. PyReconstruct Dev answers to pyrecon-dev.
• PyReconstruct Dev on macOS installs an update when you quit and reopens a few seconds later. If it cannot, the update uses the disk image as before.
• PyReconstruct Dev on Windows can install an update when you quit, without the installer. It turns on in a later Dev release; until then, updates use the installer as before.
• Help ▸ Online resources ▸ Class documents opens the class pages on pyreconstruct.org. In macOS Dev builds it is also Help ▸ Class documents.

Changed

• Security fixes for reading and writing image files, including JPEG, TIFF, PNG, GIF, PDF and EPS. Exporting a section as SVG or PNG works as before.
• Help ▸ PyReconstruct user guide now opens the guide on pyreconstruct.org. The older GitHub wiki pages stay online.
• Traces draw faster on dense sections, most of all with the whole section in view. Paging and zooming show the same picture as before.
• The name under the mouse keeps up on dense sections zoomed out. It shows the same trace as before, and paging is a little faster.
• Large series open faster. A series with half a million traces opens in about a third of the time, with the same objects and numbers as before.
• Paging through a large series no longer stalls every few sections. The pause of about a second that came every 4 to 10 section changes on a series with half a million traces is gone, and memory use is the same as before.
• Paging through the sections of a large series is faster. Stepping to the next or previous section waits less after an edit and with the whole section in view, and less for the image to open on a series with image files.

Fixed

• Status bar names with stacked accents, such as Ẫ, no longer lose their top. The alignment and brightness/contrast pills make room for the accent.
• A slow click in Combo trace mode starts a point-by-point trace. A click held longer than a moment, with a pixel or two of drift, no longer draws nothing.
• Opening another series frees the memory of the one that was open. The first series opened in a session stayed in memory until PyReconstruct quit, so a second open of a large series could double its memory use.
• An open asked for while another open runs is now skipped with a notice. The skipped series no longer leaves its working folder on disk.
• Changing sections while a series opens no longer shows a file error.
• A NUL character in the series code or a backup name now gives a clear notice. Save and close still finish, and Series ▸ Series code ▸ Set series code and File ▸ Backup ▸ Settings refuse the character.
• A close that is blocked or interrupted never leaves a series with sections missing. A backup folder inside the series' hidden working folder is no longer accepted, since a close deletes that folder.
• When a save or close fails, the window and the series stay open. Free space or close the program using the file, then save or close again.
• CSV, XML and crop log exports no longer stop on a name with a broken character. Old or damaged files can hold such a name, and the export now writes the character as text.
• Opening a series from the Finder no longer redirects or loses work. While a dialog or progress window is open, including at startup, or a series is opening, importing, saving or closing, PyReconstruct skips the open and says so.
• A series opens again after you edit an object with a broken character in its name. Old or damaged files can hold such a name, and it now stays the same through Save and reopen.
• The tool buttons no longer hide under the sliders in a short window. The brightness and contrast sliders and the section buttons move left of the tool column when it reaches down to them, so every button can be clicked.
• Save As now reports failures to move, rename or write the series. The notice says where the series and its working files are.
• On Linux, a series whose code holds a NUL character no longer freezes PyReconstruct. Its own settings, such as backups, now load and save.
• Opening a series with no series code no longer marks it as edited. Changing sections then saves nothing until you edit something.
• On Linux and Windows, a series code can no longer reach another series' settings. A code with a doubled slash or backslash, a trailing backslash, or a "." or ".." part has settings of its own.
• On Linux with Noto Sans, code in What's New matches the size of the text around it.
• The progress window closes when a legacy series import finishes or fails.

---

What's Changed

• perf(open): read section rows without building a Section by @dustenhubbard in #1100
• perf(draw): read screen points from the section's store by @dustenhubbard in #1102
• perf(open): pause the garbage collector while a series opens by @dustenhubbard in #1101
• perf(open): freeze the collector on a series after it opens by @dustenhubbard in #1104
• fix(memory): free the closed series after another opens by @dustenhubbard in #1106
• perf(open): read a large series' sections in worker processes by @dustenhubbard in #1103
• fix(open): refuse an open asked for during a running open by @dustenhubbard in #1107
• fix(open): drop a section change asked for during an open by @dustenhubbard in #1108
• perf(open): feed the workers while a first open unpacks by @dustenhubbard in #1110

Full Changelog: v1.26.0.dev202610290837...v1.26.0.dev202610300844

v1.26.0.dev202610280841

Nightly build of PyReconstruct Dev from main at ac9670b.

Changes since v1.25.0

Added

• Open a series from a terminal with pyrecon file.jser or pyreconstruct file.jser. PyReconstruct Dev answers to pyrecon-dev.
• PyReconstruct Dev on macOS installs an update when you quit and reopens a few seconds later. If it cannot, the update uses the disk image as before.
• PyReconstruct Dev on Windows can install an update when you quit, without the installer. It turns on in a later Dev release; until then, updates use the installer as before.
• Help ▸ Online resources ▸ Class documents opens the class pages on pyreconstruct.org. In macOS Dev builds it is also Help ▸ Class documents.

Changed

• Security fixes for reading and writing image files, including JPEG, TIFF, PNG, GIF, PDF and EPS. Exporting a section as SVG or PNG works as before.
• Help ▸ PyReconstruct user guide now opens the guide on pyreconstruct.org. The older GitHub wiki pages stay online.
• Traces draw faster on dense sections, most of all with the whole section in view. Paging and zooming show the same picture as before.
• The name under the mouse keeps up on dense sections zoomed out. It shows the same trace as before, and paging is a little faster.
• Paging through the sections of a large series is faster. On a series with image files, stepping to the next or previous section waits less for the image to open.

Fixed

• Status bar names with stacked accents, such as Ẫ, no longer lose their top. The alignment and brightness/contrast pills make room for the accent.
• A slow click in Combo trace mode starts a point-by-point trace. A click held longer than a moment, with a pixel or two of drift, no longer draws nothing.
• A NUL character in the series code or a backup name now gives a clear notice. Save and close still finish, and Series ▸ Series code ▸ Set series code and File ▸ Backup ▸ Settings refuse the character.
• A close that is blocked or interrupted never leaves a series with sections missing. A backup folder inside the series' hidden working folder is no longer accepted, since a close deletes that folder.
• When a save or close fails, the window and the series stay open. Free space or close the program using the file, then save or close again.
• CSV, XML and crop log exports no longer stop on a name with a broken character. Old or damaged files can hold such a name, and the export now writes the character as text.
• Opening a series from the Finder no longer redirects or loses work. While a dialog or progress window is open, including at startup, or a series is opening, importing, saving or closing, PyReconstruct skips the open and says so.
• A series opens again after you edit an object with a broken character in its name. Old or damaged files can hold such a name, and it now stays the same through Save and reopen.
• The tool buttons no longer hide under the sliders in a short window. The brightness and contrast sliders and the section buttons move left of the tool column when it reaches down to them, so every button can be clicked.
• Save As now reports failures to move, rename or write the series. The notice says where the series and its working files are.
• On Linux, a series whose code holds a NUL character no longer freezes PyReconstruct. Its own settings, such as backups, now load and save.
• Opening a series with no series code no longer marks it as edited. Changing sections then saves nothing until you edit something.
• On Linux and Windows, a series code can no longer reach another series' settings. A code with a doubled slash or backslash, a trailing backslash, or a "." or ".." part has settings of its own.
• On Linux with Noto Sans, code in What's New matches the size of the text around it.
• The progress window closes when a legacy series import finishes or fails.

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What's Changed

• docs(guide): series codes can share a backup subfolder by @dustenhubbard in #1088
• fix(save-as): move the series back when its new .jser cannot be saved by @dustenhubbard in #1087
• fix(settings): own domain on Windows for a code with an empty key name by @dustenhubbard in #1089
• chore(deps): bump dnspython from 2.8.0 to 2.9.0 by @dependabot[bot] in #1091
• chore(deps): bump pymongo from 4.18.2 to 4.18.3 by @dependabot[bot] in #1090

Full Changelog: v1.26.0.dev202610270758...v1.26.0.dev202610280841

v1.25.0

What's new in 1.25.0

New

• Customize how selected traces look in Series ▸ Options ▸ View.
• Right-click the scale bar to set its length for a figure or open its settings.
• Rename a series' images to match a zarr's image names in Series ▸ Images ▸ Find/change image directory. The zarr itself is not changed.
• On macOS, PyReconstruct ejects its installer disk image when you open the installed copy.

Improved

• PyReconstruct has a new icon.
• The scale bar resizes as you zoom, in steps of 1, 2 and 5. It is thinner, and you can set its thickness in Series ▸ Options ▸ View.
• Large series open with far less memory and save faster.
• The field redraws faster on dense sections, and changing sections is faster.
• Convert to scaled images is faster.
• Backup Settings has a checkbox for a backup folder per series.
• Help ▸ Show What's new after each update replaces Help ▸ Turn off What's new pop-up.

Fixed

• 33 fixes. Most keep your work safe: opening a zarr series no longer moves or deletes the zarr scales on disk, undo and redo keep host links and alignments, and 3D surfaces of thin objects have far fewer holes, so their area and volume change. The full list is in the changelog.

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For developers, the full technical changelog: compare v1.24.0 → v1.25.0

v1.24.0

What's new in 1.24.0

New

• Install on Linux with one command: curl -fsSL https://pyreconstruct.org/install.sh | bash. Run it again to update.
• Delete a trace from just the sections you pick with Delete from sections..., under Copy to sections....
• A palette button can fill in a new object's groups and custom columns.
• Each object can have its own smoothing window, in Edit attributes of traces....
• The object list has a 3D column. It shows which objects are in the 3D scene, and a click adds or removes one.
• An object list of only your selected traces, from Lists ▸ Object list of selected traces.
• Set auto-backup and the backup folder once for every series in File ▸ Backup ▸ Settings....
• Align a section first and propagate afterward.
• Set Attributes offers the tags already used in the series.
• Focus mode shows a label while it is on.

Improved

• The macOS app opens without the Terminal step. It is signed and notarized by Apple.
• Updates are checked against a signature before they install.
• Bug reports open with your version and system filled in.
• Every progress bar says how long is left, including the 3D scene.
• Large series use less memory and open a little faster.
• One Duplicates finder replaces the two old ones in Series ▸ Clean up.
• Updates show in the status bar instead of a dialog at launch.
• PyReconstruct Dev is a nightly build you can install beside PyReconstruct.
• What's new has a new look, is back on, and opens once after an update. To turn it off again, untick the box at the bottom or use Help ▸ Turn off What's new pop-up.

Fixed

• More than 150 fixes. Most keep your work safe: traces drawn since the last save survive more actions, Save As, undo and scissors cuts lose nothing, and zarr sizes and labels come out right. The full list is in the changelog.

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For developers, the full technical changelog: compare v1.23.0 → v1.24.0

v1.23.0

What's new in 1.23.0

New

• Double-click a .jser file to open it in PyReconstruct. This works on Windows, macOS, and
  Linux once this version is installed, and the command line takes the path directly:
  pyreconstruct series.jser.
• Hide the lists with one click. Use the sidebar button in the status bar, View ▸ Show/hide
  lists, or Cmd+Option+S (Ctrl+Alt+S on Windows and Linux), and the same toggle brings them back.
• The status bar has clickable buttons. Section, alignment, and B/C profile open their menus
  where you clicked, and the alignment and B/C profile menus can create a new entry.
• Series ▸ Clean up can repair self-crossing traces. It removes the small autoseg spikes that
  block the knife and lists true figure 8s so you can fix them with the scissors.
• Choose what the trace hover shows. Series ▸ Options ▸ View picks which object data appears,
  and in what order, for each series.
• Pin the scale bar to a length in microns. In Series ▸ Options ▸ View, a new sizing mode keeps
  the bar at a fixed µm length as you zoom, and the size slider previews on the field as you move it.
• New and remappable shortcuts. Shift+K picks the scissors and Cmd+Shift+R (Ctrl+Shift+R on
  Windows and Linux) smooths the selected traces. Align by correlation and the focus-mode edit
  click can now be changed in Help ▸ Shortcuts list.

Improved

• Large series open faster. A series with about 99,000 traces opens in about half the time, and
  the progress dialog appears before the file is read.
• Progress appears right away and says how long is left. Opening the section list and
  propagating an alignment show progress while they prepare, and recoloring objects from the
  palette shows an estimate of the time remaining.
• Lists are easier to arrange. New lists open as tabs with close buttons, floating lists are
  real windows with a "Dock this list" button, and each series remembers its list layout.
• Fewer clicks to show and hide the palettes. Right-click the scale bar, section buttons, B/C
  sliders, or trace palette to hide it. Their toggles now sit directly in the View menu, and a
  checkable menu item no longer closes its menu.
• The window opens at 70% of the screen. View ▸ Reset window puts it back there any time,
  including when it ends up off screen.
• Smaller installers. About 13 MB less to download on macOS and Windows, with nothing removed.

Changed

• Auto-merge now requires selected traces by default. The new "Only merge selected traces"
  checkbox sits beside "Automatically merge overlapping traces", including in Series ▸ Options ▸
  Mouse Tools. Uncheck it to merge any overlapping closed trace with the same name, as in 1.22.
• Eight default shortcuts moved so common keys stop colliding. For example, Options is now
  Cmd+comma, and Hide and Merge traces moved from Cmd+H and Cmd+M, which macOS reserves, to Shift+H
  and Shift+M. Help ▸ Shortcuts list shows every current key (read Cmd as Ctrl on Windows and Linux).
• The autoseg color palette has its own Colors tab. In Series ▸ Options ▸ Colors, edit colors
  with a live picker, paste several at once, and preview them on sample labels.
• The Help menu's search box replaces the Search menus row. It shows Cmd+K at its right edge
  (Ctrl+K on Windows and Linux).
• An import that cannot use the history check now says so first. Without it, deleted objects
  can come back and renamed ones can appear under both names, so the import asks before it runs.

Fixed

• Alignment edits do what you asked. Switching sections while recording alignment propagation
  no longer fails, canceling the alignment dialog also cancels a rename, and OK on an untouched
  "Edit alignment..." no longer clears the objects' alignment.
• Attributes are no longer lost. Editing trace attributes no longer resets the fill condition,
  and objects whose names contain a space or a comma keep their groups, comments, curation, and
  hosts when the series opens.
• Locked objects stay protected. "Duplicate object" and "Split into separate objects" no longer
  write into a locked object, and the scissors no longer ask "unlock it?" only to ignore the answer.
• Shortcuts that did nothing now work. Cmd+A, Cmd+D, and Cmd+Shift+I act on the list that has
  focus, Cmd+Shift+H runs Set hosts..., Cmd+Shift+D works with the object list open, and a rebound
  Home key stays rebound (Ctrl in place of Cmd on Windows and Linux).
• Fixes in the 3D scene. An opacity of 0 is kept, the scale cube keeps its edge length field
  when other objects are selected with it, and the scene redraws at the right size after moving to
  a screen with different scaling.
• Flags and series history are sturdier. Older flags keep the same identity on every open,
  so importing another user's copy merges them instead of duplicating, and a damaged row in the
  series log no longer takes good rows with it.
• A full-codebase review fixed dozens of smaller bugs. Among them: installing an optional
  package no longer freezes the window, resizing no longer zooms the view out, the z-trace commands
  are no longer grayed out, and ImageJ ROI export no longer drops traces that share a name.

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For developers, the full technical changelog: compare v1.22.3 → v1.23.0