Update docs

tberlok · Nov 3, 2023 · f6c15df · f6c15df
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diff --git a/docs/source/examples.md b/docs/source/examples.md
@@ -1,12 +1,13 @@
-# Running the examples
+# Running the examples and notebooks
 
 We provide a number of examples in the subdirectories `examples/` and `ipython-notebooks`.
-These all require some example data which can be downloaded as follows:
 
-## Downloading the example data files
+## Downloading sample data
 
-Open a terminal at the root directory of the repo, then run
+This requires some example data which can be downloaded as follows. Open a terminal at
+the root directory of the Paicos repo, then run
 ```
 wget -O data/fof_subhalo_tab_247.hdf5 https://sid.erda.dk/share_redirect/BmILDaDPPz
 wget -O data/snap_247.hdf5 https://sid.erda.dk/share_redirect/G4pUGFJUpq
-```
+```
+
diff --git a/docs/source/installation.md b/docs/source/installation.md
@@ -12,8 +12,6 @@ conda activate paicos
 
 Below we provide three differens ways of getting Paicos up and running,
 
-You will need an openmp-enabled compiler. On MacOs, you can install gcc via homebrew.
-
 ## Option 1: Compile the code and add its path to your PYTHONPATH 
 ```
 git clone git@github.com:tberlok/paicos.git
@@ -29,9 +27,30 @@ export PYTHONPATH=$PYTHONPATH:/Users/berlok/projects/paicos
 ```
 in my `.bash_profile`.
 
+#### Compiling on MacOs
+
+You will need an openmp-enabled compiler. On MacOs, you can install gcc via homebrew.
+The `setup.py` in the Paicos directory currently has the following hardcoded
+compiler option. 
+```
+if sys.platform == 'darwin':
+    os.environ['CC'] = 'gcc-13'
+    os.environ['CXX'] = 'g++-13'
+```
+If you have installed gcc via homebrew, then you can get your compiler version by running
+`brew info gcc` and update `setup.py` accordingly if that does not agree with what is hardcoded.
 
-This method can also be useful for compiling Paicos inside a Jupyter notebook, i.e.,
-by running a cell with the following content:
+
+#### Compiling Paicos inside a notebook
+It can sometimes also be useful to compile Paicos inside a Jupyter notebook, i.e.,
+by running a notebook cell with the following content:
+```
+%%bash
+
+cd /path/to/paicos/
+make clean
+make
+```
 
 ## Option 2: Installing the development version using pip 
 ```
@@ -51,7 +70,7 @@ pip install paicos
 
 ```
 # Check if installation worked and that you can import Paicos 
-python -c “import paicos”
+python -c "import paicos"
 ```
 
 ## Using openmp parallel execution of code

diff --git a/docs/source/notebooks/histogram2d.ipynb b/docs/source/notebooks/histogram2d.ipynb
diff --git a/docs/source/notebooks/histogram2d_plotting.ipynb b/docs/source/notebooks/histogram2d_plotting.ipynb
diff --git a/notebook-tutorials/paicos_examples.ipynb b/notebook-tutorials/paicos_examples.ipynb
@@ -604,7 +604,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,