Merge pull request #211 from 0Hughman0/0.3.x

0.3.x

.github/workflows/build-and-test.yml

@@ -28,7 +28,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         curl -sSL https://install.python-poetry.org | python3 -
-        poetry install
+        poetry install --all-extras
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -44,6 +44,7 @@ jobs:
     - name: Typecheck with mypy
       run: |
         poetry run mypy cassini
+        poetry run mypy tests --exclude=tests/extensions/cassini_lib/mock_libraries/ --exclude=tests/project_cases
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3
       env:

.github/workflows/python-publish.yml

@@ -32,7 +32,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         curl -sSL https://install.python-poetry.org | python3 -
-        poetry install
+        poetry install --all-extras
     - name: check tag and release version match
       shell: bash
       run: |
@@ -67,7 +67,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         curl -sSL https://install.python-poetry.org | python3 -
-        poetry install
+        poetry install --all-extras
     - name: Build package
       run: poetry build
     - name: Publish package

.gitignore

@@ -77,4 +77,4 @@ poetry.lock
 .vscode/
 
 # docs
-docs/
+/docs/

README.md

@@ -1,38 +1,29 @@
 # Cassini
 
-*Note Cassini is in it's alpha development stage, so things may not work perfectly - tell us about problems so we can fix them!*
-
 An electronic laboratory notebook (ELN), built inside Jupyter Lab.
 
 Cassini's goal is to help you explore, analyse and organise your data in an environment that's familiar.
 
-![Screenshot](demo.gif)
+https://github.com/user-attachments/assets/efd2359b-dd58-4cbc-991b-f308fe45e227
 
 ## Features
 
-* **Structures your project** into an easy to navigate hierarchy of workpackages, experiments, samples and datasets.
-* Allows **retrieval of data by name** e.g. `project['WP3.2f-XRD'] / 'XRD_data.csv`.
-* Create new sample, experiment (etc.) notebooks through **custom dialogs**.
-* Create notebook templates for **standardised proceedures**.
-* **Browse and explore** your project through a custom browser, including previewing cell outputs, such as plots in-browser.
-* No magic! Everything is stored in regular **human navigatable folders**, cloud backups etc. work as expected.
-
-Check out the demo binder for a walkthrough of features (note this can take a little while to load):
-
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/0Hughman0/Cassini/HEAD?urlpath=lab/tree/Home.ipynb)
+* **Structure your project** into a logical hierarchy _- no more lost data!_
+* **Retreive any data from anywhere**, by name _- no more copy and pasting data here there and everywhere!_
+* **Navigate and explore** your project through a fast, specialised browser _- no more endless clicking through folders!_
+* **Preview summaries of experiment parameters and results**, including graphs, temperatures, volumes, weights _- no more waiting around for notebooks to launch!_
+* **Define reusable templates** for proceedures and analysis _- no more copy and pasting code snippets!_
 
 ## Installation and Setup
 
     > pip install cassini
 
-Create a `project.py`:
+Create a `cas_project.py`:
 
-    # project.py
-    from cassini import Project, DEFAULT_TIERS
-    from cassini import jlgui
+    # cas_project.py
+    from cassini import Project, DEFAULT_TIERS    
 
     project = Project(DEFAULT_TIERS, __file__)
-    jlgui.extend_project(project)
 
     if __name__ == '__main__':
         project.launch()
@@ -41,10 +32,10 @@ And launch it:
 
     > python project.py
 
-Head to [Quickstart](https://0hughman0.github.io/Cassini/latest/quickstart.html) for more info.
+Head to [Quickstart](https://0hughman0.github.io/Cassini/0.3.x/) for more info.
 
 ## Contributing
 
-Contributing guidelines are found [here](https://0hughman0.github.io/Cassini/latest/contributing.html).
+Contributing guidelines are found [here](https://0hughman0.github.io/Cassini/0.3.x/contributing/).
 
 This includes development installation instructions and codebase orientation.

binder/Home.ipynb → binder/Introduction.ipynb

@@ -10,14 +10,14 @@
     "\n",
     "This set of notebooks serves as a walkthrough of cassini and its features.\n",
     " \n",
-    "Cassini sorts your project into a hierarchical structure, which you define your `project.py` file, which you'll find in the same folder as this notebook.\n",
+    "Cassini sorts your project into a hierarchical structure, which you define your `cas_project.py` file, which you'll find in the same folder as this notebook.\n",
     "\n",
-    "From any notebook within your project, you can import the `project` object from your `project.py` file:"
+    "From any notebook within your project, you can import the `project` object from your `cas_project.py` file:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 46,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -30,7 +30,7 @@
     }
    ],
    "source": [
-    "from project import project\n",
+    "from cas_project import project\n",
     "\n",
     "print(project.project_folder)\n",
     "print(project.hierarchy)"
@@ -86,7 +86,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -98,7 +98,7 @@
        " <DataSet \"WP1.1b-Images\">)"
       ]
      },
-     "execution_count": 32,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -109,7 +109,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -118,7 +118,7 @@
        "(<DataSet \"WP1.1b-Images\">, <DataSet \"WP1.1b-XRD\">, <DataSet \"WP1.1b-PL\">)"
       ]
      },
-     "execution_count": 34,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -139,7 +139,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -148,7 +148,7 @@
        "WindowsPath('C:/Users/ramme/Documents/Programin/WorkingVersions/cassini/dev/binder/WorkPackages/WP1/WP1.1.ipynb')"
       ]
      },
-     "execution_count": 36,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -166,16 +166,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<Meta {'description': 'First attempt.', 'started': '29/08/2023', 'conclusion': 'Not bad! Looked a bit gray though.', 'cook_time': 100} (0.0ms)>"
+       "<Meta conclusion='Not bad! Looked a bit gray though.' started=datetime.datetime(2023, 8, 29, 0, 0, tzinfo=TzInfo(UTC)) description='First attempt.' cook_time=100 (0.0ms)>"
       ]
      },
-     "execution_count": 37,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -193,7 +193,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -202,7 +202,7 @@
        "WindowsPath('C:/Users/ramme/Documents/Programin/WorkingVersions/cassini/dev/binder/WorkPackages/WP1/WP1.1/.smpls/WP1.1a.json')"
       ]
      },
-     "execution_count": 39,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -223,15 +223,13 @@
     "\n",
     "Luckily Cassini creates a bunch of helpful tools to make this as easy as possible.\n",
     "\n",
-    "First and foremost is the Cassini browser.\n",
-    "\n",
-    "This can be opened by pressing the tree button in the cassini toolbar (below the regular notebook toolbar!):\n",
+    "First and foremost is the Cassini Browser.\n",
     "\n",
-    "![tree icon](images/treeIcon.PNG)\n",
+    "This can be opened from the Launcher. Click the plus button above to open a new tab, then scroll and click the Cassini Browser Button:\n",
     "\n",
-    "**Next click the tree button**\n",
+    "![launcher icon](images/cassini-launcher.png)\n",
     "\n",
-    "**...Once it's opened, the `Home.ipynb` tab to the right of the screen to create a split view so you can keep reading this file for more instructions!**"
+    "**...Once it's opened, the `Introduction.ipynb` tab to the right of the screen to create a split view so you can keep reading this file for more instructions!**"
    ]
   },
   {
@@ -244,8 +242,6 @@
     "\n",
     "The left is the tree browser and the right the preview panel.\n",
     "\n",
-    "_you might find the preview panel gets hidden when the window resizes 😅... just click and drag from the right to restore its layout_\n",
-    "\n",
     "### The Tree Browser\n",
     "\n",
     "#### The search box\n",
@@ -270,7 +266,7 @@
     "\n",
     "You can click on the names of each tier to navigate to that tier and view its children.\n",
     "\n",
-    "The ordering of the columns can be switched by clicking on them.\n",
+    "The ordering of the rows can be switched by clicking on the column headers.\n",
     "\n",
     "### All the buttons!\n",
     "\n",
@@ -344,6 +340,8 @@
     "\n",
     "**Scroll to the Meta section**\n",
     "\n",
+    "Here you can attach meta-data to your tier.\n",
+    "\n",
     "Additional metadata can be added by clicking the add button in the meta section. \n",
     "\n",
     "![newChildIcon](images/newChildIcon.PNG)\n",
@@ -368,8 +366,6 @@
     "\n",
     "![previewIcon](images/previewIcon.PNG)\n",
     "\n",
-    "_... you might have to press it twice... for some reason 😅_\n",
-    "\n",
     "In the highlights section you should see a preview of a cell output called Photo and a nice image of a slice of toast, with a caption underneath saying 'Maybe overdone a bit'!\n",
     "\n",
     "**Click the open button to open the `WP1.1b` notebook so we can understand how that plot got there!**\n",
@@ -408,7 +404,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.8.18"
   }
  },
  "nbformat": 4,

binder/WorkPackages/.wps/WP1.json

@@ -1 +1 @@
-{"description":"Optimizing sample synthesis.\n\nThe first line of any description is taken as the 'info' which is displayed in the browser columns.","started":"29/08/2023","conclusion":"A moderate success.\n\nThe first line of the conclusion is taken as the outcome.","key":"text"}
+{"description":"Optimizing sample synthesis.\n\nThe first line of any description is taken as the 'info' which is displayed in the browser columns.","started":"2023-08-28 00:00:00Z","conclusion":"A moderate success.\n\nThe first line of the conclusion is taken as the outcome.","key":"text","temperature":100}

binder/WorkPackages/.wps/WP2.json

@@ -1 +1 @@
-{"description":"Integrating sample into device.\n\n*Markdown* is also _rendered_ in the tier preview panel.\n\nIncluding...\n\n$y = \\sin(x)$\n\nMaths!","started":"29/08/2023","conclusion":""}
+{"description":"Integrating sample into device.\n\n*Markdown* is also _rendered_ in the tier preview panel.\n\nIncluding...\n\n$y = \\sin(x)$\n\nMaths!","started":"2023-08-29 00:00:00Z","conclusion":"","temperature":150}

binder/WorkPackages/WP1.ipynb

@@ -18,7 +18,7 @@
     }
    ],
    "source": [
-    "from project import project\n",
+    "from cas_project import project\n",
     "\n",
     "wp = project.env('WP1')\n",
     "wp.gui.header()"
@@ -41,7 +41,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.8.18"
   }
  },
  "nbformat": 4,

binder/WorkPackages/WP1/.exps/WP1.1.json

@@ -1 +1 @@
-{"description":"Replicating reported method.","started":"29/08/2023","conclusion":"Reported method is nonsense.\n\nThere must be a missing step to the synthesis.\n"}
+{"description":"Replicating reported method.","started":"2023-08-28 00:00:00Z","conclusion":"Reported method is nonsense.\n\nThere must be a missing step to the synthesis.\n\nIs there something interesting that happens when this is really long, I am kinda interetted what happens. \n\nIt kinda seems like we run into some problems when this gets too long, which is kinda interesting.\n\nI am a little concerned about this and how it might go down. \n\nAlthough this seems to not be too bad in that respect, so I guess that's something! Yay!"}

binder/WorkPackages/WP1/.exps/WP1.2.json

@@ -1 +1 @@
-{"description": "Trying to use more beans.\n\nWP1.1's approach wasn't great. WP1.1d indicated could be due to a lack of beans, so going to try improving.", "started": "29/08/2023"}
+{"description": "Trying to use more beans.\n\nWP1.1's approach wasn't great. WP1.1d indicated could be due to a lack of beans, so going to try improving.", "started": "2023-08-29 00:00:00Z"}

binder/WorkPackages/WP1/WP1.1.ipynb

@@ -18,7 +18,7 @@
     }
    ],
    "source": [
-    "from project import project\n",
+    "from cas_project import project\n",
     "\n",
     "exp = project.env('WP1.1')\n",
     "exp.gui.header()"
@@ -41,7 +41,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.8.18"
   }
  },
  "nbformat": 4,

binder/WorkPackages/WP1/WP1.1/.smpls/WP1.1a.json

@@ -1 +1 @@
-{"description":"First attempt.","started":"29/08/2023","conclusion":"Not bad! Looked a bit gray though.","cook_time":100}
+{"description":"First attempt.","started":"2023-08-29 00:00:00Z","conclusion":"Not bad! Looked a bit gray though.","cook_time":100}

binder/WorkPackages/WP1/WP1.1/.smpls/WP1.1b.json

@@ -1 +1 @@
-{"description":"Trying longer cook time.\n\nFirst attempt was good. Looked a bit gray. Will trying doing for longer.","started":"29/08/2023","cook_time":12}
+{"description":"Trying longer cook time.\n\nFirst attempt was good. Looked a bit gray. Will trying doing for longer.","started":"2023-08-30 00:01:00Z","cook_time":12,"conclusion":""}

binder/WorkPackages/WP1/WP1.1/.smpls/WP1.1c.json

@@ -1 +1 @@
-{"description": "Increasing cook time.\n\n1.1b was a bit too far under.", "cook_time": "32", "started": "29/08/2023"}
+{"description":"Increasing cook time.\n\n1.1b was a bit too far under.","cook_time":32,"started":"2023-09-01 00:02:00Z"}

binder/WorkPackages/WP1/WP1.1/.smpls/WP1.1d.json

@@ -1 +1 @@
-{"description": "Just a bit more.\n\n1.1c looking good but not quite.", "cook_time": "42", "started": "29/08/2023"}
+{"description":"Just a bit more.\n\n1.1c looking good but not quite.","cook_time":42,"started":"2023-09-02 00:03:00Z"}