From ac22d4a086971051cf37caf249b7318c619b7529 Mon Sep 17 00:00:00 2001
From: Nils Brueggemann <nils.brueggemann@mpimet.mpg.de>
Date: Tue, 18 Mar 2025 22:03:39 +0100
Subject: [PATCH 1/5] setup.py and MANIFEST.in: Make sure that PyPi is not
missing the requirements.txt.
---
MANIFEST.in | 1 +
setup.py | 1 +
2 files changed, 2 insertions(+)
create mode 100644 MANIFEST.in
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..f9bd145
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1 @@
+include requirements.txt
diff --git a/setup.py b/setup.py
index 505b4f7..d545db1 100644
--- a/setup.py
+++ b/setup.py
@@ -21,6 +21,7 @@ setup(
author_email='nils.brueggemann@mpimet.mpg.de',
install_requires=install_requires,
packages=find_packages(),
+ include_package_data=True,
entry_points={
'console_scripts': [
'pyic_intake = scripts.pyic_intake:main',
--
GitLab
From aa53ba53f8af072d7e66808b891f8b6cdbb890b2 Mon Sep 17 00:00:00 2001
From: Nils Brueggemann <nils.brueggemann@mpimet.mpg.de>
Date: Tue, 18 Mar 2025 22:10:40 +0100
Subject: [PATCH 2/5] Only import ipdb if it is present.
---
pyicon/pyicon_plotting.py | 4 +++-
pyicon/pyicon_tb.py | 4 +++-
scripts/pyic_fig.py | 4 +++-
scripts/pyic_intake.py | 4 +++-
scripts/pyic_sec.py | 3 +++
scripts/pyic_view.py | 4 +++-
6 files changed, 18 insertions(+), 5 deletions(-)
diff --git a/pyicon/pyicon_plotting.py b/pyicon/pyicon_plotting.py
index 0dd734d..ec1a84e 100644
--- a/pyicon/pyicon_plotting.py
+++ b/pyicon/pyicon_plotting.py
@@ -15,7 +15,9 @@ import cartopy
import cartopy.crs as ccrs
from cartopy.mpl.ticker import LongitudeFormatter, LatitudeFormatter
import cmocean
-from ipdb import set_trace as mybreak
+import importlib.util
+if importlib.util.find_spec("ipdb"):
+ from ipdb import set_trace as mybreak
#from importlib import reload
from .pyicon_tb import write_dataarray_to_nc
from .pyicon_tb import identify_grid
diff --git a/pyicon/pyicon_tb.py b/pyicon/pyicon_tb.py
index d58ded2..9b83c69 100644
--- a/pyicon/pyicon_tb.py
+++ b/pyicon/pyicon_tb.py
@@ -18,7 +18,9 @@ import matplotlib.pyplot as plt
import matplotlib
# --- debugging
#print('mybreak')
-from ipdb import set_trace as mybreak
+import importlib.util
+if importlib.util.find_spec("ipdb"):
+ from ipdb import set_trace as mybreak
#print('pnadas')
import pandas as pd
#print('xarray')
diff --git a/scripts/pyic_fig.py b/scripts/pyic_fig.py
index 5ad9e7d..04d5837 100755
--- a/scripts/pyic_fig.py
+++ b/scripts/pyic_fig.py
@@ -166,7 +166,9 @@ def main():
import os
import sys
from pathlib import Path
- from ipdb import set_trace as mybreak
+ import importlib.util
+ if importlib.util.find_spec("ipdb"):
+ from ipdb import set_trace as mybreak
#sys.path.append(f'{Path.home()}/pyicon/')
import pyicon as pyic
print('Done loading modules.')
diff --git a/scripts/pyic_intake.py b/scripts/pyic_intake.py
index a3d2306..749d2b8 100755
--- a/scripts/pyic_intake.py
+++ b/scripts/pyic_intake.py
@@ -3,7 +3,9 @@ import os
import glob
import yaml
import argparse
-from ipdb import set_trace as mybreak
+import importlib.util
+if importlib.util.find_spec("ipdb"):
+ from ipdb import set_trace as mybreak
import sys
from netCDF4 import Dataset
import pandas as pd
diff --git a/scripts/pyic_sec.py b/scripts/pyic_sec.py
index 87c57d8..58bd3d4 100755
--- a/scripts/pyic_sec.py
+++ b/scripts/pyic_sec.py
@@ -147,6 +147,9 @@ def main():
import sys
from pathlib import Path
from ipdb import set_trace as mybreak
+ import importlib.util
+ if importlib.util.find_spec("ipdb"):
+ from ipdb import set_trace as mybreak
#sys.path.append(f'{Path.home()}/pyicon/')
import pyicon as pyic
print('Done loading modules.')
diff --git a/scripts/pyic_view.py b/scripts/pyic_view.py
index 3785dc5..eb6db36 100755
--- a/scripts/pyic_view.py
+++ b/scripts/pyic_view.py
@@ -9,7 +9,9 @@ import pyicon as pyic
import cartopy.crs as ccrs
import glob
from pyicon import params
-from ipdb import set_trace as mybreak
+import importlib.util
+if importlib.util.find_spec("ipdb"):
+ from ipdb import set_trace as mybreak
import cmocean
from pyproj import Proj, CRS, Transformer
--
GitLab
From b753de8c36bfa8030cba819c3e1302fdf0974510 Mon Sep 17 00:00:00 2001
From: Nils Brueggemann <nils.brueggemann@mpimet.mpg.de>
Date: Tue, 18 Mar 2025 22:12:02 +0100
Subject: [PATCH 3/5] requirements.txt: Move installation of ipdb and pytest to
separate file requirements_development.txt.
---
requirements.txt | 2 --
requirements_development.txt | 2 ++
2 files changed, 2 insertions(+), 2 deletions(-)
create mode 100644 requirements_development.txt
diff --git a/requirements.txt b/requirements.txt
index 4c83d1e..86b7362 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,12 +6,10 @@ xarray
pandas
cmocean
scipy
-ipdb
ipywidgets
ipykernel
jupytext
nbconvert
-pytest
healpy
cftime
#cartopy # cannot easily be installed with pip
diff --git a/requirements_development.txt b/requirements_development.txt
new file mode 100644
index 0000000..5778fd9
--- /dev/null
+++ b/requirements_development.txt
@@ -0,0 +1,2 @@
+ipdb
+pytest
\ No newline at end of file
--
GitLab
From 791fbd972cfb01730af01d3c8303289fa271e819 Mon Sep 17 00:00:00 2001
From: Nils Brueggemann <nils.brueggemann@mpimet.mpg.de>
Date: Wed, 19 Mar 2025 11:19:03 +0100
Subject: [PATCH 4/5] setup.py: Allow for more installation option.
---
setup.py | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/setup.py b/setup.py
index d545db1..37b2e0f 100644
--- a/setup.py
+++ b/setup.py
@@ -10,6 +10,12 @@ with open("README.md", "r", encoding="utf-8") as f:
with open("requirements.txt") as f:
install_requires = f.read().strip().split("\n")
+with open("requirements_documentation.txt") as f:
+ documentation_requires = f.read().strip().split("\n")
+
+with open("requirements_development.txt") as f:
+ development_requires = f.read().strip().split("\n")
+
setup(
name='pyicon-diagnostics',
version=version,
@@ -20,6 +26,11 @@ setup(
author='The pyicon development team',
author_email='nils.brueggemann@mpimet.mpg.de',
install_requires=install_requires,
+ extras_require={
+ "dev": development_requires,
+ "doc": documentation_requires,
+ "full": development_requires+documentation_requires,
+ },
packages=find_packages(),
include_package_data=True,
entry_points={
--
GitLab
From 15675b0994bbdae526fabde1e21a8123598a0b6a Mon Sep 17 00:00:00 2001
From: Nils Brueggemann <nils.brueggemann@mpimet.mpg.de>
Date: Wed, 19 Mar 2025 11:22:56 +0100
Subject: [PATCH 5/5] doc: Introduce way to install also dependencies
---
doc/doc-installation.md | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/doc/doc-installation.md b/doc/doc-installation.md
index 9406abb..fe2afa5 100644
--- a/doc/doc-installation.md
+++ b/doc/doc-installation.md
@@ -19,6 +19,12 @@ cd pyicon
pip install -e .
```
+For a more complete installation that includes dependencies for testing,
+debugging and compiling the documentation use:
+```
+pip install -e .[full]
+```
+
### On an arbitrary system
pyicon is developed for python 3.8 or later. Other versions might work as well but are not supported so far.
@@ -37,6 +43,12 @@ cd pyicon
pip install -e .
```
+For a more complete installation that includes dependencies for testing,
+debugging and compiling the documentation use:
+```
+pip install -e .[full]
+```
+
The above instructions will provide a minimum python environment that will be sufficient for most applications.
However, some more advanced features might require the installation of further python packages.
For a complete list of python packages that is supposed to cover all aspects can be obtained from the latest
--
GitLab