Fixed bugs and issues

.gitignore

@@ -132,6 +132,8 @@ dmypy.json
 docs/_build
 
 # Specific folders
+docs/notebooks
 admin
 converted
 data
+tmp

docs/intro.md

@@ -29,20 +29,20 @@ followed by running this set up command
 /global/common/software/ntrain3/ptypy_workshop_setup.sh
 ```
 
-Now that we have cloned the tutorials and set up the correct environment, we can simply navigate to ```tutorials``` in the file panel on the left and open the [first tutorial](./notebooks/Getting_Started_with_PtyPy/1_the_parameter_tree) from within the ```notebooks``` folder.
+Now that we have cloned the tutorials and set up the correct environment, we can simply navigate to ```tutorials``` in the file panel on the left and open the [first tutorial](./notebooks/01_05_Getting_Started_with_PtyPy/1_the_parameter_tree) from within the ```notebooks``` folder.
 
 
 ## How to use a Jupyter Notebook
 Before we get started with PtyPy, a few words about Jupyter Notebooks, which offer a convenient way to provide executable code (e.g. Python) alongside formatted text (using markdown). All notebooks used here are structured in the same way, with some informative content at the top and a full code example at the bottom, separated by a horizontal line:
 
 ```{figure} ./jupyter_notebook_1.PNG
-:name: jupyterlab
+:name: jupyterlab1
 ```
 
 In order to execute the code cell (or any other cell), simply select the cell and type **SHIFT+ENTER** or **ALT+ENTER**
 
 ```{figure} ./jupyter_notebook_2.PNG
-:name: jupyterlab
+:name: jupyterlab2
 ```
 
 ## Table of Contents

docs/scripts/convert.py

@@ -12,8 +12,9 @@
 if args.actions:
     notebook_dir = os.path.dirname(__file__) + "/../notebooks/"
 else:
-    notebook_dir = os.path.dirname(__file__) + "/../converted/"
+    notebook_dir = os.path.dirname(__file__) + "/../../converted/"
 notebooks = glob.glob(notebook_dir + "*/*.ipynb")
+print(notebooks, notebook_dir)
 
 def replace_div_with_admonition(cell, label="Note", type="note"):
     text = cell["source"][1:-1]
@@ -27,7 +28,8 @@ def replace_div_with_admonition(cell, label="Note", type="note"):
     new[2:2] = text
     cell["source"] = new
 
-for name in notebooks:    
+for name in notebooks:
+    print(f"Converting {name}")
     nb = json.load(open(name))
     for cell in nb["cells"]:
         if cell["cell_type"] == "markdown":

notebooks/10_13_Processing_Large_Datasets/11_multi_gpu.ipynb

@@ -29,7 +29,7 @@
    "metadata": {},
    "source": [
     "## Making a Python run script for PtyPy\n",
-    "Revisiting the earlier example on using [JSON/YAML Config Files](../01_05_Getting_Started_With_PtyPy/2_yaml_json_config.ipynb) we have saved the parameter tree from the previous example on [Working With Large Data](./10_working_with_large_data.ipynb) into a config file named [./config/dls_i08_nanogold_spiral.yml](./config/dls_i08_nanogold_spiral.yml) making a few changes, i.e. switching to ```verbose_level=info``` and providing ```p.io.rfile``` for saving the output of the reconstruction. We can then generate a simple Python script\n",
+    "Revisiting the earlier example on using [JSON/YAML Config Files](../01_05_Getting_Started_with_PtyPy/2_yaml_json_config.ipynb) we have saved the parameter tree from the previous example on [Working With Large Data](./10_working_with_large_data.ipynb) into a config file named [./config/dls_i08_nanogold_spiral.yaml](./config/dls_i08_nanogold_spiral.yaml) making a few changes, i.e. switching to ```verbose_level=info``` and providing ```p.io.rfile``` for saving the output of the reconstruction. We can then generate a simple Python script\n",
     "\n",
     "```python\n",
     "with open(\"./ptypy_run_dls_i08_nanogold.py\", \"w\") as f:\n",

notebooks/18_21_Advanced_Topics/19_live_visualisation.ipynb

@@ -18,7 +18,7 @@
    "source": [
     "## Running the reconstruction in Python script\n",
     "\n",
-    "First, we copy a YAML config file [config/dls_nanogold_spiral.yaml](config/dls_nanogold_spiral.yaml) from one of the previous examples making sure that we turn on the interaction server ```p.io.interaction.server```  \n",
+    "First, we copy a YAML config file [./config/dls_i08_nanogold_spiral.yaml](./config/dls_i08_nanogold_spiral.yaml) from one of the previous examples making sure that we turn on the interaction server ```p.io.interaction.server```  \n",
     "\n",
     "```python\n",
     "p.io = u.Param()\n",

notebooks/18_21_Advanced_Topics/20_simulating_data.ipynb

@@ -18,7 +18,7 @@
    "source": [
     "## The data\n",
     "\n",
-    "For the simulation, we can use an image of a [painting](../../data//small_data/painting.jpg) for the object and a real probe from the I08-1 instrument\n",
+    "For the simulation, we can use an image of a [painting](./_assets/painting.jpg) for the object and a real probe from the I08-1 instrument\n",
     "\n",
     "```python\n",
     "path_to_probe = \"small_data/dls_i08_nanogold_recon.ptyr\"\n",

scripts/build.sh

@@ -5,11 +5,11 @@ cd ./docs/
 cp -r ../notebooks/* ../converted/
 rm ./notebooks
 ln -s ../converted ./notebooks 
-cd ../
 
 # Convert notebooks
 module load ptypy
 python ./scripts/convert.py
 
 # Build Jupyter book
+cd ../
 jupyter-book build docs/