Merge pull request #29 from mdtanker/dev

replaced geopandas calls with pyogrio, replaced bedmap2 with bedmachine

Makefile

@@ -65,6 +65,20 @@ publish:
 package:
 	poetry build
 
+poetry_env: 
+	poetry install --sync
+	poetry export -f requirements.txt --output requirements.txt --with dev
+
+delete_env:
+	mamba remove --name antarctic_plots_dev --all --yes
+
+new_env:
+	mamba create --name antarctic_plots_dev --yes python=3.9 pygmt=0.7.0 geopandas=0.11.0
+
+install_reqs:
+	pip install --no-deps --requirement requirements.txt
+	pip install --editable .
+
 clean:
 	find . -name "*.pyc" -exec rm -v {} \;
 	find . -name ".coverage.*" -exec rm -v {} \;

antarctic_plots/maps.py

@@ -9,7 +9,7 @@
 import warnings
 from typing import Union
 
-import geopandas as gpd
+import pyogrio
 import pygmt
 
 from antarctic_plots import fetch, utils
@@ -229,7 +229,8 @@ def plot_grd(
             position=f"J{inset_pos}+j{inset_pos}+w{fig_width*.25}c",
             verbose="q",
         ):
-            gdf = gpd.read_file(fetch.groundingline())
+            # gdf = gpd.read_file(fetch.groundingline())
+            gdf = pyogrio.read_dataframe(fetch.groundingline())
             fig.plot(
                 projection=inset_map,
                 region=inset_reg,

antarctic_plots/profile.py

@@ -8,7 +8,7 @@
 
 from typing import Union
 
-import geopandas as gpd
+import pyogrio
 import numpy as np
 import pandas as pd
 import pygmt
@@ -62,7 +62,8 @@ def create_profile(
     elif method == "shapefile":
         if shapefile is None:
             raise ValueError(f"If method = {method}, need to provide a valid shapefile")
-        shp = gpd.read_file(shapefile)
+        # shp = gpd.read_file(shapefile)
+        shp = pyogrio.read_dataframe(shapefile)
         df = pd.DataFrame()
         df["coords"] = shp.geometry[0].coords[:]
         coordinates = df.coords.apply(pd.Series, index=["x", "y"])
@@ -206,16 +207,17 @@ def make_data_dict(names: list, grids: list, colors: list) -> dict:
 
 def default_layers() -> dict:
     """
-    Fetch default Bedmap2 layers.
+    Fetch default Bedmachine layers.
 
     Returns
     -------
     dict[dict]
-        Nested dictionary of Bedmap2 layers and attributes
+        Nested dictionary of Bedmachine layers and attributes
     """
-    surface = fetch.bedmap2("surface")
-    icebase = fetch.bedmap2("surface") - fetch.bedmap2("thickness")
-    bed = fetch.bedmap2("bed")
+    surface = fetch.bedmachine("surface")
+    # icebase = fetch.bedmachine("surface") - fetch.bedmachine("thickness")
+    icebase = fetch.bedmachine('icebase')
+    bed = fetch.bedmachine("bed")
     layer_names = [
         "surface",
         "icebase",
@@ -308,7 +310,7 @@ def plot_profile(
     map_cmap: str
         Change the map colorscale by passing a valid GMT cmap string, by default is 'earth'.
     map_buffer: float (0-1)
-        Change map zoom as relative percentage of profile length, by default is 0.2.
+        Change map zoom as relative percentage of profile length, by default is 0.3.
     layer_buffer: float (0-1)
         Change vertical white space within cross-section, by default is 0.1.
     data_buffer: float (0-1)
@@ -363,7 +365,7 @@ def plot_profile(
     if add_map is True:
         # Automatic data extent + buffer as % of line length
         df_reg = vd.get_region((df_layers.x, df_layers.y))
-        buffer = df_layers.dist.max() * kwargs.get("map_buffer", 0.2)
+        buffer = df_layers.dist.max() * kwargs.get("map_buffer", 0.3)
         fig_reg = utils.alter_region(df_reg, buffer=buffer)[1]
         # Set figure parameters
         fig_proj, fig_proj_ll, fig_width, fig_height = utils.set_proj(
@@ -454,7 +456,8 @@ def plot_profile(
                 position=f"J{inset_pos}+j{inset_pos}+w{fig_width*.25}c",
                 verbose="q",
             ):
-                gdf = gpd.read_file(fetch.groundingline())
+                # gdf = gpd.read_file(fetch.groundingline())
+                gdf = pyogrio.read_dataframe(fetch.groundingline())
                 fig.plot(
                     projection=inset_map,
                     region=inset_reg,

antarctic_plots/utils.py

@@ -8,7 +8,6 @@
 import warnings
 from typing import Union
 
-import geopandas as gpd
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
@@ -647,14 +646,14 @@ def raps(
             args = f"{fin} -Er+wk -Na+d -G{fout}"
             session.call_module("grdfft", args)
         if plot_type == "mpl":
-            # raps = pd.read_csv('tmp_outputs/raps.txt', header=None,
-            #     delimiter='\t',
-            #     names=('wavelength','power','stdev'))
-            # ax = sns.lineplot(raps.wavelength, raps.power,
-            #     label=j, palette='viridis')
-            # ax = sns.scatterplot(x=raps.wavelength, y=raps.power)
-            # ax.set_xlabel('Wavelength (km)')
-            # ax.set_ylabel('Radially Averaged Power ($mGal^{2}km$)')
+            raps = pd.read_csv('tmp_outputs/raps.txt', header=None,
+                delimiter='\t',
+                names=('wavelength','power','stdev'))
+            ax = sns.lineplot(raps.wavelength, raps.power,
+                label=j, palette='viridis')
+            ax = sns.scatterplot(x=raps.wavelength, y=raps.power)
+            ax.set_xlabel('Wavelength (km)')
+            ax.set_ylabel('Radially Averaged Power ($mGal^{2}km$)')
             pass
         elif plot_type == "pygmt":
             color = f"{random.randrange(255)}/{random.randrange(255)}/{random.randrange(255)}"
@@ -700,7 +699,7 @@ def coherency(grids: list, label: str, **kwargs):
     region = kwargs.get("region", None)
     spacing = kwargs.get("spacing", None)
 
-    # plt.figure()
+    plt.figure()
 
     if isinstance(grids[0], (str, xr.DataArray)):
         pygmt.grdfill(grids[0], mode="n", outgrid=f"tmp_outputs/fft_1.nc")

docs/contribute.md

@@ -1,39 +1,27 @@
 # Contribution guide
 ## Build the docs
-The Docs are build with `Sphinx` and `Read the Docs`. Due to issues with included C programs (GMT and GDAL) in a pip-installed package, `PyGMT` and `GeoPandas` aren't included in the package dependencies, so `RTD` can't run the scripts which are part of the docs (i.e. `walkthrough.ipynb`). Because of this the notebooks don't execute on a build, as specified by `execute_notebooks: 'off'` in `_config.yml`.
+The Docs are build with `Sphinx` and `Read the Docs`. Due to issues with included C programs (GMT and GDAL) in a pip-installed package, `PyGMT` and `GeoPandas` aren't included in the package dependencies, so `Read the Docs` can't run the scripts which are part of the docs (i.e. the gallery examples). Because of this the notebooks don't execute on a build, as specified by `execute_notebooks: 'off'` in `_config.yml`.
 
-Additionally we use `Poetry` as a package manager, which also can't include `PyGMT` or `GeoPandas` successfully. To get around this, we will export the poetry venv, add `PyGMT` and `Geopandas`, run the .ipynb's for the docs, then build the docs.
+Additionally we use `Poetry` as a package manager, which also can't include `PyGMT` or `GeoPandas` successfully (since it installs with Pip). To get around this, we will export the poetry venv, add `PyGMT` and `Geopandas` independently, run the .ipynb's for the docs, then build the docs.
 
 ### Set up a virtual environment
 
-Set up the poetry virutal environment:
+Set up the poetry virtual environment:
 
-    poetry install
+    make poetry_env
 
-Export to a requirements.txt:
+This solves the dependencies for the packages listed in pyproject.toml, adds the versions to a .lock file, install them in a poetry virtual environment, and exports the resulting environment to a requirements.txt file.
 
-    poetry export -f requirements.txt --output requirements.txt --dev
+Next we need to create a conda/mamba env:
+    make delete_env
+    make new_env
 
-Deactivate poetry shell:
-
-    deactivate
-
-Create a conda/mamba env:
-
-    mamba create --name antarctic_plots python=3.9 pygmt=0.7.0 geopandas=0.11.0
-    mamba activate antarctic_plots
-
-Add pinned dependencies
+This will create a new conda env `antarctic_plots_dev` and install `PyGMT`.
 
-    pip install --no-deps -r requirements.txt
-
-Install local antarctic_plots in editable mode:
-
-    pip install -e .
+Activate it and install the package requirements and local antarctic_plots package in editable mode:
 
-Or install from PyPI (docs won't update if you build them!):
-
-    pip install antarctic_plots
+    mamba activate antarctic_plots_dev
+    make install_reqs
 
 ### Run all .ipynb's to update them
 
@@ -78,14 +66,9 @@ or if the package is only for development/documentation
 
     poetry add <PACKAGE> -D
 
-Then:
-
-    poetry lock
-    poetry install <optionally add --remove-untracked>
+Then run through the commands at the top of this page again to update the environement.
 
-Note, you may need to deleted the .lock file, and run `poetry install --remove-untracked for removals to take place. This will take some time.
 
-This will solve the dependencies for the added package, re-write the `poetry.lock` file, and install the new lock file. 
 
 <!-- This uses the doc_requirements.txt included in the repository, which was create with the below code: