ibridgesgui 2.1.2__tar.gz → 2.1.3__tar.gz

{ibridgesgui-2.1.2 → ibridgesgui-2.1.3}/.github/workflows/linter.yml

@@ -12,6 +12,7 @@ on:
       - 'docs/**'
       - 'README.md'
       - '_quarto.yml'
+      - '_styles/**'
       - 'index.qmd'
       
   pull_request:
@@ -19,6 +20,7 @@ on:
       - 'docs/**'
       - 'README.md'
       - '_quarto.yml'
+      - '_styles/**'
       - 'index.qmd'
 
 jobs:

{ibridgesgui-2.1.2 → ibridgesgui-2.1.3}/.github/workflows/tests.yml

@@ -3,7 +3,19 @@ name: Tests
 on:
   push:
     branches: [main, develop]
+    paths-ignore:
+      - 'docs/**'
+      - 'README.md'
+      - '_quarto.yml'
+      - '_styles/**'
+      - 'index.qmd'
   pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'README.md'
+      - '_quarto.yml'
+      - '_styles/**'
+      - 'index.qmd'
 
 permissions:
   contents: write

{ibridgesgui-2.1.2 → ibridgesgui-2.1.3}/.gitignore

@@ -141,3 +141,7 @@ dmypy.json
 .pyre/
 
 /.quarto/
+_html/
+_site/
+
+**/*.quarto_ipynb

{ibridgesgui-2.1.2 → ibridgesgui-2.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ibridgesgui
-Version: 2.1.2
+Version: 2.1.3
 Summary: Graphical user interface for accessing data and metadata on iRODS servers.
 Author-email: Christine Staiger <c.staiger@uu.nl>
 License:                   GNU LESSER GENERAL PUBLIC LICENSE
@@ -522,7 +522,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: PySide6>=6.8.1
 Requires-Dist: ibridges<2.2,>=2.1.0
-Requires-Dist: setproctitle==1.3.7
+Requires-Dist: setproctitle==1.3.8
 Requires-Dist: importlib-resources; python_version <= "3.10"
 Requires-Dist: jsonschema
 Provides-Extra: test

ibridgesgui-2.1.3/_quarto.yml

@@ -0,0 +1,41 @@
+project:
+  type: website
+  output-dir: ./_html
+
+website:
+  title: "iBridges GUI"
+  navbar:
+    title: false
+    logo: docs/screenshots/logo.png
+    left:
+      - href: index.qmd
+        text: Home
+      - href: docs/info.qmd
+        text: What is iBridges-Gui?
+      - href: docs/getting-started.qmd
+        text: Getting started
+      - href: docs/userdoc.qmd
+        text: Documentation
+      - href: docs/developers.qmd
+        text: Contributing to iBridges
+      - href: docs/faq.qmd
+        text: FAQ
+    tools:
+      - icon: github
+        menu:
+          - text: Source Code
+            url: https://github.com/iBridges-for-iRODS/iBridges-GUI
+          - text: Report and Issue
+            url: https://github.com/iBridges-for-iRODS/iBridges-GUI/issues
+format:
+  html:
+    theme: flatly
+    css: 
+      - _styles/ibridges.css
+      - _styles/hyperlinks.css
+      - _styles/toc.css
+      - _styles/callouts.css
+      - _styles/code.css
+      - _styles/navbar.css
+      - _styles/search_icon.css
+    toc: true

ibridgesgui-2.1.3/_styles/callouts.css

@@ -0,0 +1,39 @@
+/* Base header override */
+.callout-header {
+  background-color: #a8e3d7 !important;
+}
+
+/* Note callout */
+.callout.callout-note {
+  border-left-color: #548641 !important;
+}
+
+/* Warning callout */
+.callout.callout-warning {
+  border-left-color: #E67E22 !important;
+}
+
+/* ----------------------------------------------------------
+   TIP CALLOUT — iBridges style
+   ---------------------------------------------------------- */
+
+/* Main accent colour */
+.callout.callout-tip {
+  border-left-color: #15a589 !important;
+}
+
+/* Lighter background (15a589 → lighten by ~35%) */
+.callout.callout-tip .callout-header {
+  background-color: #c8efe6 !important;  /* soft mint */
+  color: #0f7f68 !important;             /* darker accent for text */
+}
+
+/* Icon in main accent colour */
+.callout.callout-tip .callout-icon svg {
+  fill: #15a589 !important;
+}
+
+/* Body text in accent colour */
+.callout.callout-tip .callout-body {
+  color: #0f7f68 !important;
+}

ibridgesgui-2.1.3/_styles/code.css

@@ -0,0 +1,6 @@
+/* Code text color override */
+code,
+pre code,
+.reveal pre code {
+  color: #15a589 !important;
+}

ibridgesgui-2.1.3/_styles/hyperlinks.css

@@ -0,0 +1,24 @@
+/* Default link color (brand green) */
+#quarto-content a {
+  color: #58585a !important;
+  font-weight: normal;
+  text-decoration: none;
+}
+
+/* Hover: bold + darker green */
+#quarto-content a:hover {
+  color: #58585a !important;   /* darker shade derived from #528641 */
+  font-weight: bold;
+  text-decoration: underline;  /* remove if you prefer no underline */
+}
+
+/* Active (clicked) */
+#quarto-content a:active {
+  color: #58585a !important;
+  font-weight: bold;
+}
+
+/* Visited links (keep consistent) */
+#quarto-content a:visited {
+  color: #58585a !important;
+}

ibridgesgui-2.1.3/_styles/ibridges.css

@@ -0,0 +1,127 @@
+/*-- scss:defaults --*/
+
+/* Fonts */
+@import url('https://fonts.googleapis.com/css?family=Merriweather:wght@300&family=Open+Sans&display=swap');
+@import url('https://fonts.googleapis.com/css2?family=Nunito:wght@300;800&display=swap');
+
+$font-family-sans-serif: 'Nunito', Tahoma, sans-serif !default;
+
+/* Headings */
+$presentation-heading-font: 'Merriweather', Tahoma, sans-serif !default;
+$presentation-heading-color: #000000 !default;
+$h1-font-size: 3.0em !default;
+$h2-font-size: 2.7em !default;
+$h3-font-size: 2.15em !default;
+
+/*-- scss:rules --*/
+
+/* Title slide h1 */
+section.slide h1 {
+  margin-left: 5vw;
+}
+
+/* Section headings */
+section.slide h2 {
+  color: black !important;
+  background-color: #d3d3d3 !important;
+  width: 100%;
+  position: relative;
+  left: -30vw;
+
+  padding-left: 20vw;
+  padding-right: 20vw;
+  padding-top: 5px;
+  padding-bottom: 10px;
+  margin-left: 5vw;
+
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+}
+
+/* Theme section blocks */
+.theme-section {
+  text-align: left;
+  margin-top: 1.2em;
+  margin-left: 5vw;
+}
+
+/* Code blocks */
+.reveal pre code {
+  background-color: #FFFFFF;
+  font-size: 0.8em;
+  padding: 0.4em;
+  margin: 0.2em;
+}
+
+.cell {
+  margin: 1em;
+}
+
+/* Subtitle + author */
+.subtitle,
+.author {
+  color: #000000;
+  font-size: $h2-font-size;
+  font-family: $presentation-heading-font;
+}
+
+/* Footer */
+.reveal .footer {
+  color: #000000;
+  font-family: $presentation-heading-font;
+}
+
+/* Slide numbers */
+.reveal .slide-number {
+  font-family: $presentation-heading-font;
+}
+
+.slide-number {
+  bottom: 10px !important;
+  right: 10px !important;
+  top: unset !important;
+  color: #000000 !important;
+}
+
+/* Lists */
+.reveal li {
+  padding: 10px;
+}
+
+/* Center helper */
+.center-x {
+  text-align: center;
+}
+
+/* Dark background links */
+section.has-dark-background a,
+section.has-dark-background a:hover {
+  color: #d3d3d3;
+}
+
+.reveal .controls {
+  color: #15a588 !important;
+}
+
+.reveal .controls button {
+  color: #15a588 !important;
+  opacity: 1 !important; /* ensures they don’t fade */
+}
+
+.reveal .progress span {
+  background-color: #15a588 !important;
+}
+
+a,
+a:visited {
+  color: #15a588 !important;
+}
+
+a:hover,
+a:focus {
+  color: #0f7f68 !important; /* slightly darker hover */
+}
+.navbar {
+  background-color: #c8efe6 !important;
+}

ibridgesgui-2.1.3/_styles/navbar.css

@@ -0,0 +1,13 @@
+.navbar {
+  background-color: #c8efe6 !important;
+}
+/* Move tools to the left side */
+.quarto-navbar-tools {
+  order: -1 !important;
+  margin-right: 1rem !important;
+}
+
+.navbar-nav.ms-auto {
+  margin-left: auto !important; /* keep right menu spacing intact */
+}
+

ibridgesgui-2.1.3/_styles/search_icon.css

@@ -0,0 +1,13 @@
+/* Ultimate override for Quarto search icon */
+.navbar button.quarto-search-button svg,
+.navbar button.quarto-search-button svg *,
+.navbar .quarto-search-icon,
+.navbar .quarto-search-icon *,
+.navbar svg[role="img"],
+.navbar svg[role="img"] *,
+.navbar svg,
+.navbar svg * {
+  fill: #15a589 !important;
+  stroke: #15a589 !important;
+  color: #15a589 !important;
+}

ibridgesgui-2.1.3/_styles/toc.css

@@ -0,0 +1,44 @@
+/* Default TOC text (black) */
+#quarto-margin-sidebar #TOC .nav-link {
+  color: #000000 !important;
+}
+
+/* Hover state (your green) */
+#quarto-margin-sidebar #TOC .nav-link:hover {
+  color: #15a588 !important;
+}
+
+/* Active section (your green) */
+#quarto-margin-sidebar #TOC .nav-link.active {
+  color: #15a588 !important;
+  font-weight: 600;
+}
+
+/* Override Bootstrap link variables inside this TOC only */
+#quarto-margin-sidebar #TOC {
+  --bs-link-color: #000000;
+  --bs-link-hover-color: #15a588;
+  --bs-link-active-color: #15a588;
+}
+
+/* 1. Restore the original light gray left border for ALL TOC items */
+#quarto-margin-sidebar #TOC .nav-link {
+  border-left: 1px solid #dee2e6 !important;  /* original Quarto/Cosmo gray */
+  box-shadow: none !important;               /* remove Cosmo's blue shadow */
+}
+
+/* 2. Hover: green bar */
+#quarto-margin-sidebar #TOC .nav-link:hover {
+  border-left: 2px solid #15a588 !important;
+}
+
+/* 3. Active (but NOT the first item): green bar */
+#quarto-margin-sidebar #TOC ul > li:not(:first-child) > .nav-link.active {
+  border-left: 2px solid #15a588 !important;
+}
+
+/* 4. First item active: keep the light gray line, no green, no blue */
+#quarto-margin-sidebar #TOC ul > li:first-child > .nav-link.active {
+  border-left: 1px solid #dee2e6 !important;  /* restore gray */
+  box-shadow: none !important;                /* kill Cosmo's blue shadow */
+}

{ibridgesgui-2.1.2 → ibridgesgui-2.1.3}/coverage.svg

@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" width="114" height="20" role="img" aria-label="coverage: 83.18%"><title>coverage: 83.18%</title><filter id="blur"><feGaussianBlur stdDeviation="16"/></filter><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="114" height="20" rx="3"/></clipPath><g clip-path="url(#r)"><rect width="61" height="20" fill="#555"/><rect x="61" width="53" height="20" fill="#67ac09"/><rect width="114" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><g transform="scale(.1)"><g aria-hidden="true" fill="#010101"><text x="315" y="150" fill-opacity=".8" filter="url(#blur)" textLength="510">coverage</text><text x="315" y="150" fill-opacity=".3" textLength="510">coverage</text></g><text x="315" y="140" textLength="510">coverage</text></g><g transform="scale(.1)"><g aria-hidden="true" fill="#010101"><text x="865" y="150" fill-opacity=".8" filter="url(#blur)" textLength="430">83.18%</text><text x="865" y="150" fill-opacity=".3" textLength="430">83.18%</text></g><text x="865" y="140" textLength="430">83.18%</text></g></g></svg>
+<svg xmlns="http://www.w3.org/2000/svg" width="114" height="20" role="img" aria-label="coverage: 83.05%"><title>coverage: 83.05%</title><filter id="blur"><feGaussianBlur stdDeviation="16"/></filter><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="114" height="20" rx="3"/></clipPath><g clip-path="url(#r)"><rect width="61" height="20" fill="#555"/><rect x="61" width="53" height="20" fill="#67ac09"/><rect width="114" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><g transform="scale(.1)"><g aria-hidden="true" fill="#010101"><text x="315" y="150" fill-opacity=".8" filter="url(#blur)" textLength="510">coverage</text><text x="315" y="150" fill-opacity=".3" textLength="510">coverage</text></g><text x="315" y="140" textLength="510">coverage</text></g><g transform="scale(.1)"><g aria-hidden="true" fill="#010101"><text x="865" y="150" fill-opacity=".8" filter="url(#blur)" textLength="430">83.05%</text><text x="865" y="150" fill-opacity=".3" textLength="430">83.05%</text></g><text x="865" y="140" textLength="430">83.05%</text></g></g></svg>

ibridgesgui-2.1.3/docs/developers.qmd

@@ -0,0 +1,127 @@
+---
+title: "Developer Guide"
+format:
+  html:
+    toc: true
+    toc-location: right
+---
+
+## Extending iBridges‑GUI {#extending-ibridges-gui}
+
+iBridges‑GUI supports a modular plugin system that allows developers to add new functionality through custom tabs.  
+Your plugin is automatically detected and integrated into the main application at runtime.
+
+A minimal example and template structure are available in the  
+**[plugin example repository](https://github.com/iBridges-for-iRODS/ibridges-gui-tab-example)**.
+
+## Contributing {#contributing}
+
+iBridges‑GUI is an open‑source project, and we welcome contributions of all kinds — from bug reports and feature ideas to full pull requests.
+
+Main repository:  
+**[iBridges‑GUI on GitHub](https://github.com/iBridges-for-iRODS/iBridges-GUI)**
+
+### Contribution workflow
+
+1. Fork the repository  
+2. Create a feature branch from `develop`  
+3. Implement your changes  
+4. Submit a pull request back to `develop`
+
+This workflow helps us review changes efficiently and maintain a clean development history.
+
+## Code structure overview {#code-structure-overview}
+
+The core application lives in the  
+**[`ibridgesgui`](https://github.com/iBridges-for-iRODS/iBridges-GUI/tree/develop/ibridgesgui)**  
+package. Its architecture is modular, separating UI, logic, and iRODS operations into clear components.
+
+
+### Top-level modules {#top-level-modules}
+
+These modules provide the core functionality used across the application:
+
+- `__main__.py` — application entry point  
+- `config.py` — configuration handling  
+- `gui_utils.py` — shared GUI helpers  
+- `threads.py` — background worker threads  
+- `info.py` — application metadata  
+- `irods_tree_model.py` — iRODS tree model  
+- `login.py` — authentication  
+- `logviewer.py` — log viewer tab  
+- `welcome.py` — startup screen  
+- `md_schemas/` — metadata schema definitions  
+
+
+### mainmenu/ {#mainmenu}
+
+The orchestration layer of the application:
+
+- `main_window.py` — main Qt window hosting all tabs  
+- `tab_manager.py` — loads and organizes built‑in tabs  
+- `plugin_manager.py` — discovers and loads plugin tabs  
+- `session_manager.py` — manages user session state  
+- `config_manager.py` — handles configuration files and user-defined settings  
+
+This directory is the best starting point for understanding how the application is assembled.
+
+
+### browsertab/ {#browsertab}
+
+Implements the iRODS browser tab using a model–controller–view structure:
+
+- `browser_model.py` — data model  
+- `browser_controller.py` — navigation and logic  
+- `browser.py` — UI  
+- `irods_browser_service.py` — iRODS operations  
+
+
+### searchtab/ {#searchtab}
+
+Implements the search interface:
+
+- `search_model.py` — query state and results  
+- `search_controller.py` — executes searches and handles filters  
+- `search.py` — UI for building queries and viewing results  
+
+
+### synctab/ {#synctab}
+
+Implements synchronization:
+
+- `sync_model.py` — sync state and configuration  
+- `sync_controller.py` — sync logic and background tasks  
+- `sync.py` — UI for managing sync jobs  
+
+
+### popup_widgets/ {#popup-widgets}
+
+Reusable dialogs for:
+
+- creating collections  
+- creating directories  
+- uploading/downloading  
+- renaming  
+- metadata editing  
+- configuration checks  
+- resource tree dialogs  
+
+Each dialog has its own file, making them easy to reuse or extend.
+
+
+### ui_files/ {#ui-files}
+
+Contains:
+
+- Qt Designer `.ui` files  
+- auto‑generated Python wrappers  
+- matching controller/view logic  
+
+This keeps UI layout editable without touching logic.
+
+
+### icons/ {#icons}
+
+Contains all icons used in the GUI, including navigation arrows, sync indicators, loading animations, and the application logo.
+
+

ibridgesgui-2.1.3/docs/faq.qmd

@@ -0,0 +1,64 @@
+---
+title: "Frequently asked Questions"
+format:
+  html:
+    toc: false
+---
+
+If your question isn’t listed here, you may also find answers in the [**API and CLI FAQ**](https://ibridges.readthedocs.io/en/latest/faq.html).
+
+::: {.callout-tip collapse="true" title="I found a bug or have a feature request — where should I go?"}
+All development happens on **GitHub**.
+
+Check the *Issues* section to see whether your bug or idea has already been reported.  
+If not, feel free to open a new issue — we actively monitor the tracker and usually respond within a few days.
+:::
+
+::: {.callout-tip collapse="true" title="I’m getting a “NetworkError” when transferring large files"}
+This error usually appears when the **checksum calculation** exceeds the default iBridges timeout of **25,000 seconds** (~7 hours).  
+The transfer itself typically succeeds, but if the server is busy or the file is extremely large, the checksum step may run longer than the timeout.
+
+You can increase the timeout by adding this entry to your `irods_environment.json`:
+
+```
+"connection_timeout": <time in seconds>
+```
+
+The maximum allowed value is:
+
+```
+"connection_timeout": 9208512000
+```
+
+which corresponds to roughly **292 years**.
+:::
+
+::: {.callout-tip collapse="true" title="My metadata keys starting with `org_` don’t appear in iBridges"}
+iBridges hides metadata keys beginning with `org_` by default.  
+This behaviour is intentional on Yoda systems for data‑security reasons.
+
+If you need to access these keys, you can do so via the  
+[**iBridges API**](https://ibridges.readthedocs.io/en/latest/faq.html#my-metadata-with-keys-starting-with-org-do-not-show-up-in-the-ibridges-metadata).
+:::
+
+::: {.callout-tip collapse="true" title="How can I download files that match a pattern but aren’t in the same collection?"}
+Use the **Search** tab.  
+The search interface lets you filter for files regardless of their location.  
+Once the results appear, select the items you want to download.
+:::
+
+
+::: {.callout-tip collapse="true" title="How do I find all the data I have access to?"}
+Shared data in iRODS doesn’t always appear in your home or project collection.
+
+However, shared objects must always reside in a collection you can access — that’s an iRODS rule.
+
+To list all accessible collections:
+
+1. Open **Search**  
+2. Set the search path to `/yourZone/home`  
+3. Use `Obj/Coll name: %`  
+4. Select **Collections** and unselect **Data Objects**
+
+The results will show every collection you have permission to access.
+:::