Fixing small docs issues (#1893)

* fixing underlines and small code mistake * fixing issue with exporting files * fixing docstring * commenting out code and fixing links * removing hdf * fixing links * fixing overwrite issue * black fix
tardis-sn · Feb 15, 2022 · ea31f49 · ea31f49
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diff --git a/.gitignore b/.gitignore
@@ -24,6 +24,8 @@ docs/resources/ZENODO.rst
 docs/tutorials.rst
 docs/io/configuration/components/models/converters/density_parse.csv
 docs/io/configuration/components/models/converters/abund_parse.csv
+docs/io/configuration/components/models/converters/rebinned_snapshot_converted_to_tardis.csvy
+docs/io/configuration/components/models/converters/snapshot_converted_to_tardis.csvy
 
 # Eclipse editor project files
 .project

diff --git a/docs/io/configuration/components/models/converters/arepo_snapshot.hdf5 b/docs/io/configuration/components/models/converters/arepo_snapshot.hdf5
diff --git a/docs/io/configuration/components/models/converters/arepo_to_tardis.ipynb b/docs/io/configuration/components/models/converters/arepo_to_tardis.ipynb
@@ -24,7 +24,7 @@
    "id": "e3b3a256",
    "metadata": {},
    "source": [
-    "This parser is intended for loading Arepo output files ('snapshots'), extracting the relevant (line-of-sight dependent) data and exporting it to `csvy` files, which can in turn be used in TARDIS models ([see CSVY model](../index.html#csvy-model))."
+    "This parser is intended for loading Arepo output files ('snapshots'), extracting the relevant (line-of-sight dependent) data and exporting it to `csvy` files, which can in turn be used in TARDIS models ([see CSVY model](../index.rst#csvy-model))."
    ]
   },
   {
@@ -89,7 +89,7 @@
     ")\n",
     "pos, vel, rho, xnuc, time = snapshot.get_grids()\n",
     "```\n",
-    "This will load the necessary from the snapshot. See the [API](../../../../../api/tardis.io.parsers.arepo.html) documentation for more options on how to load snapshots."
+    "This will load the necessary from the snapshot. See the [API](../../../../../api/tardis.io.parsers.arepo.rst) documentation for more options on how to load snapshots."
    ]
   },
   {
@@ -257,7 +257,7 @@
    "id": "dd6310ec",
    "metadata": {},
    "source": [
-    "Once you have created a profile of the desired region, you can export the profile to a `csvy` file, which in turn can be used in a TARDIS model. Here you have to specify how many shells you want to export. The profiles are rebinned using [Scipys binned_statistic function](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binned_statistic.html), using the mean value of the data in each bin."
+    "Once you have created a profile of the desired region, you can export the profile to a `csvy` using the commented-out code below, which in turn can be used in a TARDIS model. Here you have to specify how many shells you want to export. The profiles are rebinned using [Scipys binned_statistic function](https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binned_statistic.html), using the mean value of the data in each bin."
    ]
   },
   {
@@ -267,17 +267,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "profile.export(20, \"snapshot_converted_to_tardis.csvy\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "7c4e8922",
-   "metadata": {},
-   "source": [
-    "During the export, the `yaml` header is automatically written and includes the time of the screenshot as the time for both the nuclear data as well as the density profile. Per default, the positive axis will be exported. the negative axis can be exported with `direction=\"neg\"`.\n",
-    "\n",
-    "All abundences will normalised such that roughly sum to 1, but slight deviations are expected to occur."
+    "profile.export(20, \"snapshot_converted_to_tardis.csvy\", overwrite=True)"
    ]
   },
   {
@@ -289,17 +279,23 @@
    "source": [
     "<div class=\"alert alert-info\">\n",
     "\n",
-    "\n",
-    "\n",
     "Note\n",
     "\n",
-    "\n",
-    "The export function will not overwrite existing files, but rather add an incrementing number to the filename.\n",
-    "\n",
+    "By default, the `export` method will not overwrite existing files with the same file name. Setting `overwrite=True` allows overwriting -- for example, if `overwrite=True`, if you make changes and rerun the export your exported file will be updated without creaing an additional file.\n",
     "\n",
     "</div>"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "7c4e8922",
+   "metadata": {},
+   "source": [
+    "During the export, the `yaml` header is automatically written and includes the time of the screenshot as the time for both the nuclear data as well as the density profile. Per default, the positive axis will be exported. the negative axis can be exported with `direction=\"neg\"`.\n",
+    "\n",
+    "All abundences will normalised such that roughly sum to 1, but slight deviations are expected to occur."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "5a5ec37b",
@@ -320,7 +316,7 @@
     "profile.rebin(20)\n",
     "profile.plot_profile()\n",
     "plt.show()\n",
-    "profile.export(20, \"snapshot_converted_to_tardis.csvy\", statistic=None)"
+    "profile.export(20, \"rebinned_snapshot_converted_to_tardis.csvy\", overwrite=True)"
    ]
   },
   {

diff --git a/docs/io/configuration/components/spectrum.rst b/docs/io/configuration/components/spectrum.rst
@@ -17,7 +17,7 @@ pages below:
 * virtual: :ref:`Virtual Packet Scheme <virtual_packets>`
 * integrated: :ref:`Formal Integral Method <formal_integral>`
 
-The three methods can be specified when plotting the spectrum (see the :doc:`quickstart guide <../../../quickstart/quickstart>` for an example of this).
+The three methods can be specified when plotting the spectrum (see the :doc:`quickstart guide <../../../quickstart>` for an example of this).
 
 The following example shows how to edit variables for the different methods. 
 

diff --git a/tardis/io/parsers/arepo.py b/tardis/io/parsers/arepo.py
@@ -279,7 +279,7 @@ class Profile:
     def __init__(self, pos, vel, rho, xnuc, time):
         """
         Parameters
-        -----
+        ----------
         pos : list of float
             Meshgrid of positions in center of mass frames in
             Cartesian coordinates
@@ -321,15 +321,15 @@ def plot_profile(self, save=None, dpi=600, **kwargs):
         Plots profile, both in the positive and negative direction.
 
         Parameters
-        -----
+        ----------
         save : str
             Path under which the figure is to be saved. Default: None
         dpi : int
             Dpi of the saved figure
         **kwargs : keywords passable to matplotlib.pyplot.plot()
 
         Returns
-        -----
+        -------
         fig : matplotlib figure object
         """
 
@@ -413,14 +413,14 @@ def rebin(self, nshells, statistic="mean"):
         by passing the statistics="std" keyword.
 
         Parameters
-        -----
+        ----------
         nshells : int
             Number of bins of new data.
         statistic : str
             Scipy keyword for scipy.stats.binned_statistic. Default: mean
 
         Returns
-        -----
+        -------
         self : Profile object
 
         """
@@ -474,15 +474,22 @@ def rebin(self, nshells, statistic="mean"):
 
         return self
 
-    def export(self, nshells, filename, direction="pos", statistic="mean"):
+    def export(
+        self,
+        nshells,
+        filename,
+        direction="pos",
+        statistic="mean",
+        overwrite=False,
+    ):
         """
         Function to export a profile as csvy file. Either the
-        positive or negative direction can be exported. Does
-        not overwrite existing files, saves to *(<n>).csvy
+        positive or negative direction can be exported. By default
+        does not overwrite existing files, saves to <filename>_<number>.csvy
         file instead.
 
         Parameters
-        -----
+        ----------
         nshells : int
             Number of shells to be exported.
         filename : str
@@ -494,9 +501,12 @@ def export(self, nshells, filename, direction="pos", statistic="mean"):
         statistic : str
             Scipy keyword for scipy.stats.binned_statistic. If
             statistic=None, data is not rebinned. Default: "mean"
+        overwrite: bool
+            If true, will overwrite if a file of the same name exists.
+            By default False.
 
         Returns
-        -----
+        -------
         filename : str
             Name of the actual saved file
         """
@@ -505,7 +515,7 @@ def export(self, nshells, filename, direction="pos", statistic="mean"):
         if filename.endswith(".csvy"):
             filename = filename.replace(".csvy", "")
 
-        if os.path.exists("%s.csvy" % filename):
+        if os.path.exists("%s.csvy" % filename) and not overwrite:
             i = 0
             while os.path.exists("%s_%s.csvy" % (filename, i)):
                 i += 1
@@ -598,7 +608,7 @@ def export(self, nshells, filename, direction="pos", statistic="mean"):
 
         return filename
 
-    def get_profiles():
+    def get_profiles(self):
         """Returns all profiles for manual post_processing etc."""
         return (
             self.pos_prof_p,
@@ -630,7 +640,7 @@ def create_profile(
         Creates a profile along the x-axis
 
         Parameters
-        -----
+        ----------
         inner_radius : float
             Inner radius where the profiles will be cut off. Default: None
         outer_radius : float
@@ -644,7 +654,7 @@ def create_profile(
             Dpi of the saved plot. Default: 600
 
         Returns
-        -----
+        -------
         profile : LineProfile object
 
         """
@@ -771,7 +781,7 @@ def create_profile(
         Creates a profile along the x-axis without any averaging
 
         Parameters
-        -----
+        ----------
         opening_angle : float
             Opening angle (in degrees) of the cone from which the
             data is extracted. Refers to the total opening angle, not
@@ -789,7 +799,7 @@ def create_profile(
             Dpi of the saved plot. Default: 600
 
         Returns
-        -----
+        -------
         profile : LineProfile object
 
         """
@@ -932,7 +942,7 @@ def create_profile(
         direction are identical.
 
         Parameters
-        -----
+        ----------
         inner_radius : float
             Inner radius where the profiles will be cut off. Default: None
         outer_radius : float
@@ -946,7 +956,7 @@ def create_profile(
             Dpi of the saved plot. Default: 600
 
         Returns
-        -----
+        -------
         profile : LineProfile object
 
         """