Docs for tui version release (#334)

* Starting tidying up the website and adding how-to for install and choosing terminal. * Add first draft of walkthrough. * Full thread through and text tidy up, add all internal and external links. * Add textual-dev to dev dependencies. * Delete test screenshot svgs. * Testing resoltuion after 300 dpi in photoshop. * Trying 600 dpi. * Trying 1200 dpi! * try with shareX * Check how things render on macos few figures added. * Adding screenshots for graphical interface part of walkthrough. * Adding python API sections to walkthrough. * First draft of the tutorial complete. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Continue drafting + dark mode datashuttle image. * Adding pictures to HOW TO. * Export dark mode datashuttle as artboard. * Upload halfway through transfer page, need to check. * Rough draft complete for all sections. * something went wrong with git. * finish first draft of all how-tos. * Rename 'make_folders' to 'create_folders' in docs. * First draft of docs complete. * Add notes on taking screenshots. * Minor formatting changes, improvements during doc writing. * Remove high dpi screenshots that were slowing down git. * Fix tests after DataShuttle changed to datashuttle. * Fix top-level folder widget test. * Fix errors introduced after API changes. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
neuroinformatics-unit · Apr 8, 2024 · 849efa6 · 849efa6
1 parent 0a9f549
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diff --git a/datashuttle/tui/app.py b/datashuttle/tui/app.py
@@ -43,7 +43,7 @@ class TuiApp(App):
 
     def compose(self) -> ComposeResult:
         yield Container(
-            Label("DataShuttle", id="mainwindow_banner_label"),
+            Label("datashuttle", id="mainwindow_banner_label"),
             Button(
                 "Select Existing Project",
                 id="mainwindow_existing_project_button",
@@ -118,7 +118,7 @@ def handle_open_filesystem_browser(self, path_: Path) -> None:
                 )
             else:
                 message = (
-                    "Unexpected error occurred. Please contact the DataShuttle"
+                    "Unexpected error occurred. Please contact the datashuttle"
                     "development team."
                 )
 

diff --git a/datashuttle/tui/configs.py b/datashuttle/tui/configs.py
@@ -443,15 +443,15 @@ def setup_configs_for_a_new_project(self) -> None:
                 ).disabled = False
 
                 message = (
-                    "A DataShuttle project has now been created.\n\n "
+                    "A datashuttle project has now been created.\n\n "
                     "Next, setup the SSH connection. Once complete, navigate to the "
                     "'Main Menu' and proceed to the project page, where you will be "
                     "able to create and transfer project folders."
                 )
 
             else:
                 message = (
-                    "A DataShuttle project has now been created.\n\n "
+                    "A datashuttle project has now been created.\n\n "
                     "Next proceed to the project page, where you will be "
                     "able to create and transfer project folders."
                 )

diff --git a/datashuttle/tui/css/tui_menu.tcss b/datashuttle/tui/css/tui_menu.tcss
@@ -13,7 +13,7 @@
 #mainwindow_banner_label {
     border: hkey $primary;
     content-align: center middle;
-    text-style: italic bold;
+    text-style: bold;
     color: $text;
     width: 50%;
     height: 5;

diff --git a/datashuttle/utils/rclone.py b/datashuttle/utils/rclone.py
@@ -285,8 +285,8 @@ def assert_rclone_check_output_is_as_expected(result, symbol, convert_symbols):
     assert symbol in convert_symbols.keys(), "rclone check symbol is unknown."
     assert symbol != "!", (
         "Could not complete rlcone check. "
-        "This is unexpected. Please contact DataShuttle "
-        "devs at our GitHub page."
+        "This is unexpected. Please contact datashuttle "
+        "at our GitHub page."
     )
 
 

diff --git a/datashuttle/utils/ssh.py b/datashuttle/utils/ssh.py
@@ -129,13 +129,11 @@ def setup_ssh_key(
     """
     if not sys.stdin.isatty():
         utils.log_and_raise_error(
-            f"Attempting to run outside of a TTY terminal. "
-            f"This may happen if attempting to run in an IDE console. "
-            f"`getpass` (used for ssh password input) cannot run. "
-            f"Try running using the command-line-interface with "
-            f"'datashuttle {cfg.project_name} "
-            f"setup-ssh-connection-to-central-server' "
-            f"or in a terminal rather than IDE console.",
+            "Attempting to run outside of a TTY terminal. "
+            "This may happen if attempting to run in an IDE console. "
+            "`getpass` (used for ssh password input) cannot run. "
+            "Try using Python from the operating system "
+            "terminal to run this function.",
             RuntimeError,
         )
 

diff --git a/docs/rebuild.py b/docs/rebuild.py
@@ -0,0 +1,10 @@
+import shutil
+import subprocess
+from pathlib import Path
+
+build_path = Path(__file__).parent / "build"
+
+if build_path.is_dir():
+    shutil.rmtree(build_path)
+
+subprocess.run("sphinx-build ./source ./build", shell=True)
diff --git a/docs/source/_static/NeuroBlueprint_project_tree_dark.png b/docs/source/_static/NeuroBlueprint_project_tree_dark.png
diff --git a/docs/source/_static/NeuroBlueprint_project_tree_light.png b/docs/source/_static/NeuroBlueprint_project_tree_light.png
diff --git a/docs/source/_static/css/custom.css b/docs/source/_static/css/custom.css
@@ -46,3 +46,7 @@ html[data-theme=light] {
   height: auto;
   margin: 5px auto;
 }
+
+.center {
+    text-align: center;
+}
diff --git a/docs/source/_static/datashuttle-overview-dark.png b/docs/source/_static/datashuttle-overview-dark.png
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diff --git a/docs/source/_static/screenshots/how-to-create-project-ssh-light.png b/docs/source/_static/screenshots/how-to-create-project-ssh-light.png
diff --git a/docs/source/_static/screenshots/how-to-logs-filesbrowser-dark.png b/docs/source/_static/screenshots/how-to-logs-filesbrowser-dark.png
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diff --git a/docs/source/_static/screenshots/how-to-transfer-custom-dark.png b/docs/source/_static/screenshots/how-to-transfer-custom-dark.png
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diff --git a/docs/source/_static/screenshots/updating-configs-dark.png b/docs/source/_static/screenshots/updating-configs-dark.png
diff --git a/docs/source/_static/screenshots/updating-configs-light.png b/docs/source/_static/screenshots/updating-configs-light.png
diff --git a/docs/source/_static/tutorial-1-example-file-tree-dark.png b/docs/source/_static/tutorial-1-example-file-tree-dark.png
diff --git a/docs/source/_static/tutorial-1-example-file-tree-light.png b/docs/source/_static/tutorial-1-example-file-tree-light.png
diff --git a/docs/source/_static/tutorial-1-explore-folders-dark.png b/docs/source/_static/tutorial-1-explore-folders-dark.png
diff --git a/docs/source/_static/tutorial-1-explore-folders-light.png b/docs/source/_static/tutorial-1-explore-folders-light.png
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -62,6 +62,8 @@
     "strikethrough",
     "substitution",
     "tasklist",
+    "attrs_block",  # https://stackoverflow.com/questions/78183173/custom-styling-a-header-in-sphinx-website?noredirect=1#comment137843002_78183173
+    "attrs_inline"
 ]
 # Automatically add anchors to markdown headings
 myst_heading_anchors = 3
@@ -152,6 +154,7 @@
     },
     "footer_start": ["footer_start"],
     "footer_end": ["footer_end"],
+    "show_prev_next": False,
     "show_toc_level": 2,  # sidebar levels that are expanded before scrolling
 #    "secondary_sidebar_items": [],
  #   "page_sidebar_items": [],

diff --git a/docs/source/index.md b/docs/source/index.md
@@ -1,48 +1,69 @@
 :html_theme.sidebar_secondary.remove:
 
-# DataShuttle Documentation
+{.center}
+# **datashuttle**
 
-This website includes the documentation and API documentation for DataShuttle.
+<p style="text-align: center; font-size: 22px;">The tool to automate neuroscience project folder creation and transfer.</p>
 
-For additional information, please visit the [GitHub Page](https://github.com/neuroinformatics-unit/datashuttle).
-
-Any feedback is much appreciated, please open at [GitHub Issue](https://github.com/neuroinformatics-unit/datashuttle/issues)
-or join our [Zulip chat](https://neuroinformatics.zulipchat.com/#narrow/stream/405999-DataShuttle) if you have any problems or suggestions.
-
-## Explore the Documentation
+```{image} _static/datashuttle-overview-light.png
+:alt: My Logo
+:class: logo, mainlogo, only-light
+:align: center
+:width: 600px
+```
+```{image} _static/datashuttle-overview-dark.png
+:alt: My Logo
+:class: logo, mainlogo, only-dark
+:align: center
+:width: 600px
+```
+<br>
 
 ::::{grid} 1 2 2 3
-:gutter: 3
+:gutter: 4
 
-:::{grid-item-card} User Guide
-:link: pages/documentation
+:::{grid-item-card} Tutorials
+:link: pages/tutorials
 :link-type: doc
 
-Get started with DataShuttle.
+Walkthrough **datashuttle**.
+:::
+
+:::{grid-item-card} How To
+:link: pages/how_tos
+:link-type: doc
 
+Short guides on specific actions.
 :::
 
 :::{grid-item-card} Python API
 :link: pages/api_index
 :link-type: doc
 
-Check out the API reference.
+Full Python API reference.
 :::
+::::
 
-:::{grid-item-card} Command-line interface
-:link: pages/cli_index
-:link-type: doc
+Datashuttle creates and validates projects standardised to the
+[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev)
+specification.
 
-Use datashuttle with the CLI.
-:::
+Dive right into **datashuttle** with our
+[Getting Started Tutorial]((tutorial-getting-started)=)
+or targeted [How-To Guides](how-tos).
+
+Don't hesitate to get in contact through our
+[GitHub Issues](https://github.com/neuroinformatics-unit/datashuttle/issues)
+or
+[Zulip Chat.](https://neuroinformatics.zulipchat.com/#narrow/stream/405999-DataShuttle)
 
-::::
 
 ```{toctree}
 :maxdepth: 2
 :caption: index
 :hidden:
 
-pages/documentation
+pages/tutorials
+pages/how_tos
 pages/api_index
 ```
diff --git a/docs/source/pages/documentation.md b/docs/source/pages/documentation.md
@@ -399,79 +399,6 @@ necessary for SSH transfer.
 Next, we can start setting up the project by automatically creating standardised
 project folder trees.
 
-# Creating *subject* and *session* folders
-
-In a typical neuroscience experiment, data collection sessions begin by
-creating the folder for the current *subject* (e.g. mouse, rat) and current *session*.
-
-The command `create-folders` can be used to automatically create standardised
-folder trees (see
-[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/) for details on the standardisation scheme).
-
-
-An example project directory for the behavioural data for the first *subject*,
-first *session* of an experiment may look like:
-
-```
-└── my_first_project/
-    └── rawdata/
-        └── sub-001/
-            └── ses-001_date-20230516/
-                └── behav
-```
-
-In Datashuttle, this folder tree can be created with the below command
-(assuming today's date is `20230516`):
-
-::::{tab-set}
-
-:::{tab-item} Python API
-```{code-block} python
-project.create_folders(
-	sub_names="001",
-	ses_names="001_@DATE@",
-	datatype="behav"
-)
-```
-:::
-
-:::{tab-item} CLI (macOS / Linux)
-```{code-block} console
-datashuttle \
-my_first_project \
-create-folders -sub 001 -ses 001_@DATE@ -dt behav
-```
-:::
-
-:::{tab-item} CLI (Windows)
-```{code-block} console
-datashuttle ^
-my_first_project ^
-create-folders -sub 001 -ses 001_@DATE@ -dt behav
-```
-:::
-
-::::
-
-The leading `sub-` or `ses-` in the provided *subject* and *session* names
-are optional in the command, these prefixes
-will always be added
-(i.e. both `-sub 001` and `-sub sub-001` are valid inputs).
-
-It is possible to automatically create date, time or datetime key-value pairs with the tags
-`@DATE@`, `@TIME@` or `@DATETIME@` respectively.
-A range of *subjects* and *sessions* can be created with the `@TO@` flag.
-See the [convenience tags](#convenience-tags) section for more details.
-
-
-## *Datatype* Folders
-
-*Datatype* folders contain acquired experimental data and must be named either
-`behav`, `ephys`, `funcimg` or `anat`. *Datatype* folders must be placed
-within a *session* folder.
-See the [*datatype*](https://neuroblueprint.neuroinformatics.dev/specification.html#datatype) section
-of NeuroBlueprint for details.
-
 # Data Transfer
 
 Datashuttle offers a convenient way of transferring entire project folders or
@@ -650,6 +577,7 @@ For example, the command:
 :::{tab-item} Python API
 ```{code-block} python
 project.create_folders(
+    top_level_folder="rawdata",
 	sub_names="sub-001",
 	ses_names=["001_@DATETIME@", "002_@DATETIME@"],
 	datatype="behav",
@@ -1008,6 +936,7 @@ The command:
 :::{tab-item} Python API
 ```{code-block} python
 project.create_folders(
+    top_level_folder="rawdata",
 	sub_names="001",
 	ses_names="all",
 	datatype="all_datatype"
@@ -1054,6 +983,7 @@ but not the non-*datatype* file `ses-001_extra-file.json`.
 :::{tab-item} Python API
 ```{code-block} python
 project.create_folders(
+    top_level_folder="rawdata",
 	sub_names="all_non_sub",
 	ses_names="all",
 	datatype="all"

diff --git a/docs/source/pages/how_tos.md b/docs/source/pages/how_tos.md
@@ -0,0 +1,72 @@
+:html_theme.sidebar_secondary.remove:
+(how-tos)=
+# How To
+
+## Get Started
+
+::::{grid} 1 1 2 2
+:gutter: 4
+
+:::{grid-item-card} {fas}`desktop;sd-text-primary` Install
+:link: how_tos/install
+:link-type: doc
+
+How to install **datashuttle**
+:::
+
+:::{grid-item-card} {fas}`desktop;sd-text-primary` Choose a Terminal
+:link: how_tos/choose-a-terminal
+:link-type: doc
+
+Choose the best terminal to run the graphical interface.
+:::
+
+:::{grid-item-card} {fas}`desktop;sd-text-primary` Make a New Project
+:link: how_tos/make-a-new-project
+:link-type: doc
+
+Full details on setting up a new project.
+:::
+
+::::
+
+## Manage your project
+::::{grid} 1 1 2 2
+:gutter: 4
+
+:::{grid-item-card} {fas}`desktop;sd-text-primary` Create Folders
+:link: how_tos/create-folders
+:link-type: doc
+
+All you need to know about creating folders.
+:::
+
+:::{grid-item-card} {fas}`desktop;sd-text-primary` Transfer Data
+:link: how_tos/transfer-data
+:link-type: doc
+
+The ultimate guide to data-transfer.
+:::
+
+:::{grid-item-card} {fas}`desktop;sd-text-primary` Update Configs
+:link: how_tos/update-configs
+:link-type: doc
+
+Changing an existing project's configurations.
+:::
+
+:::{grid-item-card} {fas}`desktop;sd-text-primary` Read the Logs
+:link: how_tos/read-logs
+:link-type: doc
+
+How to access full logs of everything **datashuttle** does.
+:::
+
+:::{grid-item-card} {fas}`desktop;sd-text-primary` Use Name Templates
+:link: how_tos/use-name-templates
+:link-type: doc
+
+A handy feature for template subject and session names.
+:::
+
+::::