Packaging and example data download module

MANIFEST.in

@@ -1,2 +1,2 @@
-include pydartdiags/obs_sequence/composite_types.yaml
+include src/pydartdiags/obs_sequence/composite_types.yaml
 

docs/api/example_data.rst

@@ -0,0 +1,9 @@
+.. example_data:
+
+=====================
+module: data
+=====================
+
+.. automodule:: data
+   :members:
+   :member-order: bysource

docs/api/index.rst

@@ -12,3 +12,4 @@ API Guide
     stats
     matplots
     plots
+    example_data

examples/01_manipulating/plot_duplicates.py

@@ -9,15 +9,14 @@
 
 ###########################################
 # Import the obs_sequence module
-import os
 import pydartdiags.obs_sequence.obs_sequence as obsq
+from pydartdiags.data import get_example_data
 
 ###########################################
 # Read in the observation sequence file. In this example we'll use a real obs_seq file,
-# the NCEP+ACARS.201303_6H.obs_seq2013030306 file that comes with the pyDARTdiags package.
+# the NCEP+ACARS.201303_6H.obs_seq2013030306 file.
 # This is 6 hours of observations from March 3, 2013.
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file = os.path.join(data_dir, "NCEP+ACARS.201303_6H.obs_seq2013030306")
+data_file = get_example_data("NCEP+ACARS.201303_6H.obs_seq2013030306")
 
 obs_seq = obsq.ObsSequence(data_file)
 

examples/01_manipulating/plot_external_fo.py

@@ -16,16 +16,15 @@
 
 ###########################################
 # Import the obs_sequence module, and numpy
-import os
 import pydartdiags.obs_sequence.obs_sequence as obsq
+from pydartdiags.data import get_example_data
 import numpy as np
 
 ###########################################
 # Read in the observation sequence file. In this example we'll use the
-# obs_seq.out.tracer file that comes with the pyDARTdiags package.
-# This file only has two observations. 
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file = os.path.join(data_dir, "obs_seq.out.tracer")
+# obs_seq.out.tracer file.
+# This file only has two observations.
+data_file = get_example_data("obs_seq.out.tracer")
 obs_seq = obsq.ObsSequence(data_file)
 
 ###########################################

examples/01_manipulating/plot_join_obs_seq.py

@@ -10,15 +10,12 @@
 ###########################################
 # Import the obs_sequence module.
 import pydartdiags.obs_sequence.obs_sequence as obsq
+from pydartdiags.data import get_example_data
 
 ###########################################
 # Chose the first obs_seq file to read.
-# In this example, we are using a small obs_seq file "obs_seq.final.1000"
-# that comes with the pyDARTdiags package 
-# in the data directory, so we ``import os`` to get the path to the file.
-import os
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file1 = os.path.join(data_dir, "obs_seq.final.1000")
+# In this example, we are using a small obs_seq file "obs_seq.final.1000".
+data_file1 = get_example_data("obs_seq.final.1000")
 
 ###########################################
 # Read the obs_seq file into an obs_seq object.
@@ -30,7 +27,7 @@
 ###########################################
 # Chose the second obs_seq file to read.
 
-data_file2 = os.path.join(data_dir, "obs_seq.final.ascii.small")
+data_file2 = get_example_data("obs_seq.final.ascii.small")
 obs_seq2 = obsq.ObsSequence(data_file2)
 
 print('obs_seq2 has assimilation info:', obs_seq2.has_assimilation_info())

examples/01_manipulating/plot_remove_obs.py

@@ -10,15 +10,12 @@
 ###########################################
 # Import the obs_sequence module
 import pydartdiags.obs_sequence.obs_sequence as obsq
+from pydartdiags.data import get_example_data
 
 ###########################################
 # Chose an obs_seq file to read.
-# In this example, we are using a small obs_seq file "obs_seq.final.medium"
-# that comes with the pyDARTdiags package 
-# in the data directory, so we ``import os`` to get the path to the file.
-import os
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file = os.path.join(data_dir, "obs_seq.final.ascii.medium")
+# In this example, we are using a small obs_seq file "obs_seq.final.medium".
+data_file = get_example_data("obs_seq.final.ascii.medium")
 
 ###########################################
 # Read the obs_seq file into an obs_seq object.

examples/02_visualizing/plot_qc_hover.py

@@ -13,20 +13,17 @@
 
 ###########################################
 # Import the modules
-import os
 import plotly.express as px
 import pydartdiags.obs_sequence.obs_sequence as obsq
+from pydartdiags.data import get_example_data
 
 # sphinx_gallery_thumbnail_path = '_static/geo_thumb.png'
 
 
 ###########################################
 # Read the obs_seq file into an obs_seq object.
-# In this example, we use a small obs_seq file "obs_seq.final.ascii.medium"
-# that comes with the pyDARTdiags package 
-# in the data directory, so we use ``os`` to get the path to the file
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file = os.path.join(data_dir, "obs_seq.final.ascii.medium")
+# In this example, we use a small obs_seq file "obs_seq.final.ascii.medium".
+data_file = get_example_data("obs_seq.final.ascii.medium")
 
 obs_seq = obsq.ObsSequence(data_file)
 

examples/03_diagnostics/plot_evolution.py

@@ -11,16 +11,13 @@
 # and the matplots module for plotting.
 import pydartdiags.obs_sequence.obs_sequence as obsq
 from pydartdiags.matplots import matplots as mp
+from pydartdiags.data import get_example_data
 
 ###########################################
 # Chose an obs_seq file to read.
 # In this example, we are using "obs_seq.final.lorenz_96" which is from
 # a Lorenz 96 model run with the DART assimilation system.
-# The obs_seq.final.lorenz_96 file comes with the pyDARTdiags package
-# in the data directory, so we ``import os`` to get the path to the file.
-import os
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file = os.path.join(data_dir, "obs_seq.final.lorenz_96")
+data_file = get_example_data("obs_seq.final.lorenz_96")
 
 ###########################################
 # Read the obs_seq file into an obs_seq object.

examples/03_diagnostics/plot_grand_stats.py

@@ -13,14 +13,12 @@
 # and the statistics module.
 import pydartdiags.obs_sequence.obs_sequence as obsq
 from pydartdiags.stats import stats
+from pydartdiags.data import get_example_data
+
 ###########################################
 # Chose an obs_seq file to read.
-# This is a small obs_seq file "obs_seq.final.ascii.medium"
-# that comes with the pyDARTdiags package 
-# in the data directory, so we ``import os`` to get the path to the file
-import os
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file = os.path.join(data_dir, "obs_seq.final.ascii.medium")
+# This is a small obs_seq file "obs_seq.final.ascii.medium".
+data_file = get_example_data("obs_seq.final.ascii.medium")
 
 
 ###########################################

examples/03_diagnostics/plot_profiles.py

@@ -12,15 +12,12 @@
 # and the matplots module for plotting.
 import pydartdiags.obs_sequence.obs_sequence as obsq
 from pydartdiags.matplots import matplots as mp
+from pydartdiags.data import get_example_data
 
 ###########################################
 # Chose an obs_seq file to read.
-# In this example, we are using a small obs_seq file "obs_seq.final.1000"
-# that comes with the pyDARTdiags package 
-# in the data directory, so we ``import os`` to get the path to the file.
-import os
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file = os.path.join(data_dir, "obs_seq.final.1000")
+# In this example, we are using a small obs_seq file "obs_seq.final.1000".
+data_file = get_example_data("obs_seq.final.1000")
 
 ###########################################
 # Read the obs_seq file into an obs_seq object.

examples/03_diagnostics/plot_qc_poss_vs_used.py

@@ -12,15 +12,12 @@
 ###########################################
 # Import the obs_sequence module
 import pydartdiags.obs_sequence.obs_sequence as obsq
+from pydartdiags.data import get_example_data
 
 ###########################################
 # Chose an obs_seq file to read.
-# This is a small obs_seq file "obs_seq.final.ascii.small"
-# that comes with the pyDARTdiags package 
-# in the data directory, so we ``import os`` to get the path to the file
-import os
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file = os.path.join(data_dir, "obs_seq.final.ascii.small")
+# This is a small obs_seq file "obs_seq.final.ascii.small".
+data_file = get_example_data("obs_seq.final.ascii.small")
 
 ###########################################
 # read the obs_seq file into an obs_seq object

examples/03_diagnostics/plot_rank_histogram.py

@@ -12,15 +12,12 @@
 # and the matplots module for plotting.
 import pydartdiags.obs_sequence.obs_sequence as obsq
 from pydartdiags.matplots import matplots as mp
+from pydartdiags.data import get_example_data
 
 ###########################################
 # Chose an obs_seq file to read.
-# In this example, we are using a small obs_seq file "obs_seq.final.1000"
-# that comes with the pyDARTdiags package 
-# in the data directory, so we ``import os`` to get the path to the file.
-import os
-data_dir = os.path.join(os.getcwd(), "../..", "data")
-data_file = os.path.join(data_dir, "obs_seq.final.1000")
+# In this example, we are using a small obs_seq file "obs_seq.final.1000".
+data_file = get_example_data("obs_seq.final.1000")
 
 ###########################################
 # Read the obs_seq file into an obs_seq object.

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "wheel"]
+requires = ["setuptools>=64", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -29,3 +29,6 @@ Homepage = "https://github.com/NCAR/pyDARTdiags.git"
 Issues = "https://github.com/NCAR/pyDARTdiags/issues"
 Documentation = "https://ncar.github.io/pyDARTdiags"
 
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["pydartdiags*"]