From 015547da005e5b3fd18d60cdb8c3c726d3dcb62e Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 12:27:28 +0000
Subject: [PATCH 01/19] introduce pyproject.toml

---
 pyproject.toml | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..64fa647
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,44 @@
+[build-system]
+requires = ["setuptools >= 40.9.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cso"
+version = "0.1.dev0"
+authors = [{ name = "Arjo Segers" }]
+description = "CAMS Satellite Operator (CSO) tool."
+readme = "README.md"
+classifiers = [
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: MIT",
+    "Operating System :: OS Independent",
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Education",
+    "Topic :: Scientific/Engineering :: Atmospheric Science",
+]
+requires-python = ">=3.10"
+
+dependencies = [
+    "cartopy>=0.20",
+    "shapely",
+    "numpy",
+    "matplotlib",
+    "numba",
+    "pandas",
+    "tqdm",
+    "xarray",
+    "netcdf4",
+    "scipy >=1.1.0",
+    "requests",
+    "typer",
+]
+
+[project.urls]
+Home = "https://ci.tno.nl/gitlab/cams/cso"
+
+[project.optional-dependencies]
+docs = ["pre-commit"]
-- 
GitLab


From 3bba4c74dd42c4074d5691be709c9f35c0471ca8 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 12:28:07 +0000
Subject: [PATCH 02/19] update README.md

---
 README.md | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/README.md b/README.md
index ef6dcfc..0b75cba 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,32 @@ Note that the documenation requires 'sphinx',
 which is usually part of your python distribution.
 
 
+Installation from source
+------------------------
+
+CSO can be installed from source in either conda or virtual environments.
+
+**Pip**
+
+The file py_project.toml contains the dependencies needed by CSO.  
+
+    python3 -m venv --prompt cso .venv
+
+This will create a new Python evironment folder called `cso`. To activate it run
+
+    source .venv/bin/activate
+
+You may need to updated pip with the command
+
+    pip install -U pip
+
+We can then install CSO and its dependencies simply using pip
+
+    pip install -e .
+
+The `-e` flag installs CSO in editable mode, meaning that the user can change the source code and run CSO anywhere using these changes.
+
+
 Tutorial
 --------
 
-- 
GitLab


From d990b01b7757ef4a2c8aaa2cc5d9cade7335ebf6 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 12:28:45 +0000
Subject: [PATCH 03/19] introduce .pre-commit-config-yaml

---
 .pre-commit-config.yaml | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..1e75fd8
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,6 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.5.5
+  hooks:
+    - id: ruff-format
+    - id: ruff # linter
\ No newline at end of file
-- 
GitLab


From bcd925434d7c61c2b72d4c013f721e0353ece632 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 12:29:35 +0000
Subject: [PATCH 04/19] add build to gitignore

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index 3132557..53a7a82 100644
--- a/.gitignore
+++ b/.gitignore
@@ -28,3 +28,6 @@ ENV/
 env.bak/
 venv.bak/
 .vscode
+
+#packaging
+build/
\ No newline at end of file
-- 
GitLab


From 4a4ae2d1143691f69ebcb0eb7fc7b889762f6c90 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 12:51:17 +0000
Subject: [PATCH 05/19] shuffle things about

---
 src/cso/__init__.py                    |  0
 {py => src/cso}/cso.py                 |  0
 {py => src/cso}/cso_catalogue.py       |  0
 {py => src/cso}/cso_colhub.py          |  0
 {py => src/cso}/cso_colocate.py        |  0
 {py => src/cso}/cso_constants.py       |  0
 {py => src/cso}/cso_dataspace.py       |  0
 {py => src/cso}/cso_earthaccess.py     |  0
 {py => src/cso}/cso_file.py            |  0
 {py => src/cso}/cso_gridded.py         |  0
 {py => src/cso}/cso_inquire.py         |  0
 {py => src/cso}/cso_mapping.py         |  0
 {py => src/cso}/cso_pal.py             |  0
 {py => src/cso}/cso_plot.py            |  0
 {py => src/cso}/cso_regions.py         |  0
 {py => src/cso}/cso_s5p.py             |  0
 {py => src/cso}/cso_superobs.py        |  0
 {py => src/cso}/cso_tools.py           |  0
 src/cso/scripts/__init__.py            |  0
 src/cso/scripts/cli.py                 | 96 ++++++++++++++++++++++++++
 src/utopya/__init__.py                 |  0
 {py => src/utopya}/rc.py               |  0
 {py => src/utopya}/utopya.py           |  0
 {py => src/utopya}/utopya_base.py      |  0
 {py => src/utopya}/utopya_build.py     |  0
 {py => src/utopya}/utopya_index.py     |  0
 {py => src/utopya}/utopya_jobscript.py |  0
 {py => src/utopya}/utopya_jobtree.py   |  0
 {py => src/utopya}/utopya_post.py      |  0
 {py => src/utopya}/utopya_rc.py        |  0
 {py => src/utopya}/utopya_runscript.py |  0
 {py => src/utopya}/utopya_tools.py     |  0
 32 files changed, 96 insertions(+)
 create mode 100644 src/cso/__init__.py
 rename {py => src/cso}/cso.py (100%)
 rename {py => src/cso}/cso_catalogue.py (100%)
 rename {py => src/cso}/cso_colhub.py (100%)
 rename {py => src/cso}/cso_colocate.py (100%)
 rename {py => src/cso}/cso_constants.py (100%)
 rename {py => src/cso}/cso_dataspace.py (100%)
 rename {py => src/cso}/cso_earthaccess.py (100%)
 rename {py => src/cso}/cso_file.py (100%)
 rename {py => src/cso}/cso_gridded.py (100%)
 rename {py => src/cso}/cso_inquire.py (100%)
 rename {py => src/cso}/cso_mapping.py (100%)
 rename {py => src/cso}/cso_pal.py (100%)
 rename {py => src/cso}/cso_plot.py (100%)
 rename {py => src/cso}/cso_regions.py (100%)
 rename {py => src/cso}/cso_s5p.py (100%)
 rename {py => src/cso}/cso_superobs.py (100%)
 rename {py => src/cso}/cso_tools.py (100%)
 create mode 100644 src/cso/scripts/__init__.py
 create mode 100644 src/cso/scripts/cli.py
 create mode 100644 src/utopya/__init__.py
 rename {py => src/utopya}/rc.py (100%)
 rename {py => src/utopya}/utopya.py (100%)
 rename {py => src/utopya}/utopya_base.py (100%)
 rename {py => src/utopya}/utopya_build.py (100%)
 rename {py => src/utopya}/utopya_index.py (100%)
 rename {py => src/utopya}/utopya_jobscript.py (100%)
 rename {py => src/utopya}/utopya_jobtree.py (100%)
 rename {py => src/utopya}/utopya_post.py (100%)
 rename {py => src/utopya}/utopya_rc.py (100%)
 rename {py => src/utopya}/utopya_runscript.py (100%)
 rename {py => src/utopya}/utopya_tools.py (100%)

diff --git a/src/cso/__init__.py b/src/cso/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/py/cso.py b/src/cso/cso.py
similarity index 100%
rename from py/cso.py
rename to src/cso/cso.py
diff --git a/py/cso_catalogue.py b/src/cso/cso_catalogue.py
similarity index 100%
rename from py/cso_catalogue.py
rename to src/cso/cso_catalogue.py
diff --git a/py/cso_colhub.py b/src/cso/cso_colhub.py
similarity index 100%
rename from py/cso_colhub.py
rename to src/cso/cso_colhub.py
diff --git a/py/cso_colocate.py b/src/cso/cso_colocate.py
similarity index 100%
rename from py/cso_colocate.py
rename to src/cso/cso_colocate.py
diff --git a/py/cso_constants.py b/src/cso/cso_constants.py
similarity index 100%
rename from py/cso_constants.py
rename to src/cso/cso_constants.py
diff --git a/py/cso_dataspace.py b/src/cso/cso_dataspace.py
similarity index 100%
rename from py/cso_dataspace.py
rename to src/cso/cso_dataspace.py
diff --git a/py/cso_earthaccess.py b/src/cso/cso_earthaccess.py
similarity index 100%
rename from py/cso_earthaccess.py
rename to src/cso/cso_earthaccess.py
diff --git a/py/cso_file.py b/src/cso/cso_file.py
similarity index 100%
rename from py/cso_file.py
rename to src/cso/cso_file.py
diff --git a/py/cso_gridded.py b/src/cso/cso_gridded.py
similarity index 100%
rename from py/cso_gridded.py
rename to src/cso/cso_gridded.py
diff --git a/py/cso_inquire.py b/src/cso/cso_inquire.py
similarity index 100%
rename from py/cso_inquire.py
rename to src/cso/cso_inquire.py
diff --git a/py/cso_mapping.py b/src/cso/cso_mapping.py
similarity index 100%
rename from py/cso_mapping.py
rename to src/cso/cso_mapping.py
diff --git a/py/cso_pal.py b/src/cso/cso_pal.py
similarity index 100%
rename from py/cso_pal.py
rename to src/cso/cso_pal.py
diff --git a/py/cso_plot.py b/src/cso/cso_plot.py
similarity index 100%
rename from py/cso_plot.py
rename to src/cso/cso_plot.py
diff --git a/py/cso_regions.py b/src/cso/cso_regions.py
similarity index 100%
rename from py/cso_regions.py
rename to src/cso/cso_regions.py
diff --git a/py/cso_s5p.py b/src/cso/cso_s5p.py
similarity index 100%
rename from py/cso_s5p.py
rename to src/cso/cso_s5p.py
diff --git a/py/cso_superobs.py b/src/cso/cso_superobs.py
similarity index 100%
rename from py/cso_superobs.py
rename to src/cso/cso_superobs.py
diff --git a/py/cso_tools.py b/src/cso/cso_tools.py
similarity index 100%
rename from py/cso_tools.py
rename to src/cso/cso_tools.py
diff --git a/src/cso/scripts/__init__.py b/src/cso/scripts/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/cso/scripts/cli.py b/src/cso/scripts/cli.py
new file mode 100644
index 0000000..27e5c13
--- /dev/null
+++ b/src/cso/scripts/cli.py
@@ -0,0 +1,96 @@
+import subprocess
+from typing import Optional
+
+import typer
+import sys
+import os
+import webbrowser
+
+from cso import __package__, __version__
+
+# import utopya
+
+# prefix of CSO installation:
+prefix = os.path.abspath(os.path.join(os.path.dirname(sys.argv[0]), os.pardir))
+# extend path:
+sys.path.insert(0, os.path.join(prefix, "src/cso"))
+sys.path.insert(0, os.path.join(prefix, "src/utopya"))
+
+main = typer.Typer()
+
+
+def version_callback(value: bool):
+    if not value:
+        return
+    typer.echo(f"🛰️  {__package__} {__version__}")
+    raise typer.Exit()
+
+
+@main.callback()
+def callback(
+    version: Optional[bool] = typer.Option(None, "--version", "-V", callback=version_callback),
+):
+    """🛰️  CAMS Satellite Operator (CSO) Command Line Interface"""
+
+@main.command()
+def run(rc_file: str = typer.Argument(..., help="Provide .rc file")):
+    """Run cso based on settings provided in .rc file (e.g., cso run config/tutorial/tutorial.rc)"""
+    raise NotImplementedError
+    # # set environment:
+    # os.environ["CSO_PREFIX"] = prefix
+    # # dummy values to ensure that settings could be read first to setup logging:
+    # os.environ["CSO_RCFILE"] = "None"
+    # os.environ["CSO_RCDIR"] = "None"
+
+    # # init script:
+    # utos = utopya.UtopyaRunScriptRc()
+
+    # # setup standard command line arguments, and also enable rcfile arguments:
+    # utos.ArgumentsSetup(description="CAMS Satellite Operator", rcbase="cso")
+
+    # # evaluate known arguments, store the other ;
+    # # might show help text and exit:
+    # args, xargs = utos.ArgumentsParse()
+
+    # # store full path to settings:
+    # os.environ["CSO_RCFILE"] = os.path.abspath(args.rcfile)
+    # # location of settings file:
+    # os.environ["CSO_RCDIR"] = os.path.dirname(os.path.abspath(args.rcfile))
+
+    # # start, shout info:
+    # logging.info(f"")
+    # logging.info(f"** CSO - CAMS Satellite Operator **")
+    # logging.info(f"")
+    # logging.info(f"installation prefix  : {prefix}")
+    # logging.info(f"input rcfile         : {args.rcfile}")
+    # logging.info(f"settings base        : {args.rcbase}")
+    # logging.info(f"")
+    # logging.info(f"environment:")
+    # for key in ["CSO_PREFIX", "CSO_RCFILE", "CSO_RCDIR"]:
+    #     logging.info(f"  {key} = {os.environ[key]}")
+    # # endfor
+    # logging.info(f"")
+
+    # # info ...
+    # logging.info(f"start job tree ...")
+    # # import class as defined in settings by 'cso.class' key;
+    # # should be (derived from) 'utopya.JobStep' :
+    # jbs_cls = utos.ImportClass("class")
+    # # init job step object, use the 'rcbase' as name:
+    # jbs = jbs_cls(args.rcbase, args.rcfile)
+    # # start first:
+    # jbs.Start(single=args.single)
+
+    # # info:
+    # logging.info(f"")
+    # logging.info(f"** end **")
+    # logging.info(f"")
+
+
+# -------------------------------------------------
+# end
+# -------------------------------------------------
+
+
+if __name__ == "__main__":
+    main()
diff --git a/src/utopya/__init__.py b/src/utopya/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/py/rc.py b/src/utopya/rc.py
similarity index 100%
rename from py/rc.py
rename to src/utopya/rc.py
diff --git a/py/utopya.py b/src/utopya/utopya.py
similarity index 100%
rename from py/utopya.py
rename to src/utopya/utopya.py
diff --git a/py/utopya_base.py b/src/utopya/utopya_base.py
similarity index 100%
rename from py/utopya_base.py
rename to src/utopya/utopya_base.py
diff --git a/py/utopya_build.py b/src/utopya/utopya_build.py
similarity index 100%
rename from py/utopya_build.py
rename to src/utopya/utopya_build.py
diff --git a/py/utopya_index.py b/src/utopya/utopya_index.py
similarity index 100%
rename from py/utopya_index.py
rename to src/utopya/utopya_index.py
diff --git a/py/utopya_jobscript.py b/src/utopya/utopya_jobscript.py
similarity index 100%
rename from py/utopya_jobscript.py
rename to src/utopya/utopya_jobscript.py
diff --git a/py/utopya_jobtree.py b/src/utopya/utopya_jobtree.py
similarity index 100%
rename from py/utopya_jobtree.py
rename to src/utopya/utopya_jobtree.py
diff --git a/py/utopya_post.py b/src/utopya/utopya_post.py
similarity index 100%
rename from py/utopya_post.py
rename to src/utopya/utopya_post.py
diff --git a/py/utopya_rc.py b/src/utopya/utopya_rc.py
similarity index 100%
rename from py/utopya_rc.py
rename to src/utopya/utopya_rc.py
diff --git a/py/utopya_runscript.py b/src/utopya/utopya_runscript.py
similarity index 100%
rename from py/utopya_runscript.py
rename to src/utopya/utopya_runscript.py
diff --git a/py/utopya_tools.py b/src/utopya/utopya_tools.py
similarity index 100%
rename from py/utopya_tools.py
rename to src/utopya/utopya_tools.py
-- 
GitLab


From d88d4b35b33419d5a91c6fe053cb1e643841cd17 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:05:52 +0000
Subject: [PATCH 06/19] update gitignore

---
 .gitignore             |  4 +++-
 src/utopya/__init__.py | 11 +++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 53a7a82..a0af670 100644
--- a/.gitignore
+++ b/.gitignore
@@ -28,6 +28,8 @@ ENV/
 env.bak/
 venv.bak/
 .vscode
+.tmp
 
 #packaging
-build/
\ No newline at end of file
+build/
+src/cso.egg-info/*
\ No newline at end of file
diff --git a/src/utopya/__init__.py b/src/utopya/__init__.py
index e69de29..cbc5b19 100644
--- a/src/utopya/__init__.py
+++ b/src/utopya/__init__.py
@@ -0,0 +1,11 @@
+
+from .utopya_base import *
+from .utopya_rc import *
+from .utopya_jobscript import *
+from .utopya_jobtree import *
+from .utopya_runscript import *
+
+# from utopya_install    import *
+from .utopya_tools import *
+from .utopya_index import *
+from .utopya_post import *
\ No newline at end of file
-- 
GitLab


From 9cbd8af03ba17183a4b6b0ed2012b7d61843e710 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:07:07 +0000
Subject: [PATCH 07/19] introduce CLI in pyproject.toml

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 64fa647..f19894e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,3 +42,6 @@ Home = "https://ci.tno.nl/gitlab/cams/cso"
 
 [project.optional-dependencies]
 docs = ["pre-commit"]
+
+[project.scripts]
+cso = "cso.scripts.cli:main"
-- 
GitLab


From ac214c5df80dd89d01c2100163965fa94c665c59 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:09:37 +0000
Subject: [PATCH 08/19] mv rc.py

---
 src/{utopya => }/rc.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename src/{utopya => }/rc.py (100%)

diff --git a/src/utopya/rc.py b/src/rc.py
similarity index 100%
rename from src/utopya/rc.py
rename to src/rc.py
-- 
GitLab


From 49c7d0e474433ae2eb02a509fa3c4c7a3349b0f4 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:09:52 +0000
Subject: [PATCH 09/19] new dev version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index f19894e..b48864c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cso"
-version = "0.1.dev0"
+version = "0.1.dev1"
 authors = [{ name = "Arjo Segers" }]
 description = "CAMS Satellite Operator (CSO) tool."
 readme = "README.md"
-- 
GitLab


From bfe1fcb17fa71264ad78d9425396dae94bb773fc Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:25:52 +0000
Subject: [PATCH 10/19] use relative import in subpackages

---
 src/cso/__init__.py            | 19 +++++++++++++++++++
 src/cso/cso_catalogue.py       | 14 +++++++-------
 src/cso/cso_colhub.py          |  4 ++--
 src/cso/cso_colocate.py        |  6 +++---
 src/cso/cso_dataspace.py       |  2 +-
 src/cso/cso_earthaccess.py     |  4 ++--
 src/cso/cso_gridded.py         |  6 +++---
 src/cso/cso_inquire.py         |  2 +-
 src/cso/cso_pal.py             |  2 +-
 src/cso/cso_regions.py         | 14 +++++++-------
 src/cso/cso_s5p.py             | 16 ++++++++--------
 src/cso/cso_superobs.py        |  4 ++--
 src/utopya/utopya.py           | 18 +++++++++---------
 src/utopya/utopya_build.py     | 12 ++++++------
 src/utopya/utopya_index.py     |  4 ++--
 src/utopya/utopya_jobscript.py |  2 +-
 src/utopya/utopya_jobtree.py   | 14 +++++++-------
 src/utopya/utopya_post.py      |  2 +-
 src/utopya/utopya_rc.py        |  2 +-
 src/utopya/utopya_runscript.py |  4 ++--
 20 files changed, 85 insertions(+), 66 deletions(-)

diff --git a/src/cso/__init__.py b/src/cso/__init__.py
index e69de29..3ce8f6d 100644
--- a/src/cso/__init__.py
+++ b/src/cso/__init__.py
@@ -0,0 +1,19 @@
+from importlib import metadata
+
+__version__ = metadata.version(__package__)
+
+from .cso_file import *
+from .cso_catalogue import *
+from .cso_inquire import *
+
+# from .cso_scihub import *
+from .cso_pal import *
+from .cso_s5p import *
+from .cso_superobs import *
+from .cso_gridded import *
+from .cso_colocate import *
+from .cso_superobs import *
+from .cso_regions import *
+from .cso_constants import *
+from .cso_mapping import *
+from .cso_plot import *
\ No newline at end of file
diff --git a/src/cso/cso_catalogue.py b/src/cso/cso_catalogue.py
index 4b49d8f..e27d04b 100644
--- a/src/cso/cso_catalogue.py
+++ b/src/cso/cso_catalogue.py
@@ -114,7 +114,7 @@ class CSO_CatalogueBase(utopya.UtopyaRc):
         import numpy
 
         # tools:
-        import cso_constants
+        from . import cso_constants
 
         # no target units defined?
         if (vunits is None) or (vunits == "None"):
@@ -278,8 +278,8 @@ class CSO_Catalogue(CSO_CatalogueBase):
         import matplotlib.pyplot as plt
 
         # tools:
-        import cso_file
-        import cso_plot
+        from . import cso_file
+        from . import cso_plot
 
         # setup graphics back-end:
         matplotlib.use("Agg")
@@ -660,8 +660,8 @@ class CSO_SimCatalogue(CSO_CatalogueBase):
         import matplotlib.pyplot as plt
 
         # tools:
-        import cso_file
-        import cso_plot
+        from . import cso_file
+        from . import cso_plot
 
         # setup graphics back-end:
         matplotlib.use("Agg")
@@ -1008,8 +1008,8 @@ class CSO_GriddedCatalogue(CSO_CatalogueBase):
         import matplotlib.pyplot as plt
 
         # tools:
-        import cso_file
-        import cso_plot
+        from . import cso_file
+        from . import cso_plot
 
         # setup graphics back-end:
         matplotlib.use("Agg")
diff --git a/src/cso/cso_colhub.py b/src/cso/cso_colhub.py
index 26aff59..8f179ec 100644
--- a/src/cso/cso_colhub.py
+++ b/src/cso/cso_colhub.py
@@ -148,7 +148,7 @@ class CSO_ColHubMirror_Inquire(utopya.UtopyaRc):
         import fnmatch
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # info ...
         logging.info(f"{indent}")
@@ -375,7 +375,7 @@ class CSO_ColHubMirror_Missing(utopya.UtopyaRc):
         import fnmatch
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # info ...
         logging.info(f"{indent}")
diff --git a/src/cso/cso_colocate.py b/src/cso/cso_colocate.py
index 8b208ab..24a7b05 100644
--- a/src/cso/cso_colocate.py
+++ b/src/cso/cso_colocate.py
@@ -56,7 +56,7 @@ import logging
 
 # tools:
 import utopya
-import cso_catalogue
+from . import cso_catalogue
 
 
 ########################################################################
@@ -191,8 +191,8 @@ class CSO_CoLocate(utopya.UtopyaRc):
         import xarray
 
         # tools:
-        import cso_file
-        import cso_mapping
+        from . import cso_file
+        from . import cso_mapping
 
         # init base object:
         utopya.UtopyaRc.__init__(self, rcfile, rcbase=rcbase, env=env)
diff --git a/src/cso/cso_dataspace.py b/src/cso/cso_dataspace.py
index e240a90..8250df3 100644
--- a/src/cso/cso_dataspace.py
+++ b/src/cso/cso_dataspace.py
@@ -776,7 +776,7 @@ class CSO_DataSpace_Downloader(object):
         import shutil
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # no token yet?
         if self.access_token is None:
diff --git a/src/cso/cso_earthaccess.py b/src/cso/cso_earthaccess.py
index 74cbefb..c147774 100644
--- a/src/cso/cso_earthaccess.py
+++ b/src/cso/cso_earthaccess.py
@@ -158,7 +158,7 @@ class CSO_EarthAccess_Inquire(utopya.UtopyaRc):
         import pandas
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # info ...
         logging.info(f"{indent}")
@@ -491,7 +491,7 @@ class CSO_EarthAccess_Download(utopya.UtopyaRc):
         import earthaccess
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # info ...
         logging.info(f"{indent}")
diff --git a/src/cso/cso_gridded.py b/src/cso/cso_gridded.py
index b5f0182..ca7b4c9 100644
--- a/src/cso/cso_gridded.py
+++ b/src/cso/cso_gridded.py
@@ -267,8 +267,8 @@ class CSO_GriddedAverage(utopya.UtopyaRc):
         import pandas
 
         # tools:
-        import cso_file
-        import cso_mapping
+        from . import cso_file
+        from . import cso_mapping
 
         # init base object:
         utopya.UtopyaRc.__init__(self, rcfile, rcbase=rcbase, env=env)
@@ -1210,7 +1210,7 @@ class CSO_GriddedAverageMeans(utopya.UtopyaRc):
         import pandas
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # init base object:
         utopya.UtopyaRc.__init__(self, rcfile, rcbase=rcbase, env=env)
diff --git a/src/cso/cso_inquire.py b/src/cso/cso_inquire.py
index 9c19a0f..dc1ecae 100644
--- a/src/cso/cso_inquire.py
+++ b/src/cso/cso_inquire.py
@@ -151,7 +151,7 @@ class CSO_Inquire_Plot(utopya.UtopyaRc):
         import matplotlib.dates as mdates
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # setup graphics back-end:
         matplotlib.use("Agg")
diff --git a/src/cso/cso_pal.py b/src/cso/cso_pal.py
index 502991a..e13aefc 100644
--- a/src/cso/cso_pal.py
+++ b/src/cso/cso_pal.py
@@ -397,7 +397,7 @@ class CSO_PAL_Downloader(object):
         import requests
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # retry loop ..
         ntry = 1
diff --git a/src/cso/cso_regions.py b/src/cso/cso_regions.py
index d8db155..1424620 100644
--- a/src/cso/cso_regions.py
+++ b/src/cso/cso_regions.py
@@ -74,7 +74,7 @@ import logging
 
 # tools:
 import utopya
-import cso_catalogue
+from . import cso_catalogue
 
 
 ########################################################################
@@ -1703,9 +1703,9 @@ class CSO_Catalogue_RegionsMaps(cso_catalogue.CSO_CatalogueBase):
         import matplotlib.pyplot as plt
 
         # tools:
-        import cso_file
-        import cso_plot
-        import cso_regions
+        from . import cso_file
+        from . import cso_plot
+        from . import cso_regions
 
         # setup graphics back-end:
         matplotlib.use("Agg")
@@ -2063,9 +2063,9 @@ class CSO_Catalogue_RegionsTimeSeries(cso_catalogue.CSO_CatalogueBase):
         import xarray
 
         # tools:
-        import cso_file
-        import cso_plot
-        import cso_regions
+        from . import cso_file
+        from . import cso_plot
+        from . import cso_regions
 
         # setup graphics back-end:
         matplotlib.use("Agg")
diff --git a/src/cso/cso_s5p.py b/src/cso/cso_s5p.py
index 60976ac..ed3dcf8 100644
--- a/src/cso/cso_s5p.py
+++ b/src/cso/cso_s5p.py
@@ -123,7 +123,7 @@ import logging
 
 # tools:
 import utopya
-import cso_file
+from . import cso_file
 
 
 ########################################################################
@@ -2724,9 +2724,9 @@ class CSO_S5p_Convert(utopya.UtopyaRc):
         import pandas
 
         # tools:
-        import cso_file
-        import cso_dataspace
-        import cso_pal
+        from . import cso_file
+        from . import cso_dataspace
+        from . import cso_pal
         import utopya
 
         # info ...
@@ -3231,8 +3231,8 @@ class CSO_S5p_Download(utopya.UtopyaRc):
         import pandas
 
         # tools:
-        import cso_dataspace
-        import cso_pal
+        from . import cso_dataspace
+        from . import cso_pal
 
         # info ...
         logging.info(f"{indent}")
@@ -3559,7 +3559,7 @@ class CSO_S5p_Listing(utopya.UtopyaRc):
         import glob
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # info ...
         logging.info(f"{indent}")
@@ -3786,7 +3786,7 @@ class CSO_S5p_Download_Listing(utopya.UtopyaRc):
         import collections
 
         # tools:
-        import cso_file
+        from . import cso_file
 
         # info ...
         logging.info(f"{indent}")
diff --git a/src/cso/cso_superobs.py b/src/cso/cso_superobs.py
index a0d3394..79a75a6 100644
--- a/src/cso/cso_superobs.py
+++ b/src/cso/cso_superobs.py
@@ -191,8 +191,8 @@ class CSO_SuperObs(utopya.UtopyaRc):
         import pandas
 
         # tools:
-        import cso_file
-        import cso_mapping
+        from . import cso_file
+        from . import cso_mapping
 
         # init base object:
         utopya.UtopyaRc.__init__(self, rcfile, rcbase=rcbase, env=env)
diff --git a/src/utopya/utopya.py b/src/utopya/utopya.py
index 277ea0f..5fc65dc 100644
--- a/src/utopya/utopya.py
+++ b/src/utopya/utopya.py
@@ -152,15 +152,15 @@ and are defined according to the following hierchy:
 # imports from sub modules
 # -------------------------------------------------
 
-from utopya_base import *
-from utopya_rc import *
-from utopya_jobscript import *
-from utopya_jobtree import *
-from utopya_runscript import *
-from utopya_tools import *
-from utopya_build import *
-from utopya_index import *
-from utopya_post import *
+from .utopya_base import *
+from .utopya_rc import *
+from .utopya_jobscript import *
+from .utopya_jobtree import *
+from .utopya_runscript import *
+from .utopya_tools import *
+from .utopya_build import *
+from .utopya_index import *
+from .utopya_post import *
 
 
 # -------------------------------------------------
diff --git a/src/utopya/utopya_build.py b/src/utopya/utopya_build.py
index 69f7f08..8231fc9 100644
--- a/src/utopya/utopya_build.py
+++ b/src/utopya/utopya_build.py
@@ -106,7 +106,7 @@ Classes
 import logging
 
 # tools:
-import utopya_rc
+from . import utopya_rc
 
 
 # -------------------------------------------------
@@ -303,7 +303,7 @@ class UtopyaCopy(utopya_rc.UtopyaRc):
         import os
 
         # tools:
-        import utopya_tools
+        from . import utopya_tools
 
         # init base object:
         utopya_rc.UtopyaRc.__init__(self, rcfile=rcfile, rcbase=rcbase, env=env)
@@ -797,7 +797,7 @@ class UtopyaConfigure(utopya_rc.UtopyaRc):
         import glob
 
         # tools:
-        import utopya_tools
+        from . import utopya_tools
 
         # info ...
         logging.info("configure source code ...")
@@ -1236,7 +1236,7 @@ class UtopyaConfigure(utopya_rc.UtopyaRc):
         """
 
         # tools:
-        import utopya_tools
+        from . import utopya_tools
 
         # info...
         logging.info("  macro definitions ...")
@@ -2496,7 +2496,7 @@ class UtopyaDependencies(utopya_rc.UtopyaRc):
         """
 
         # tools:
-        import utopya_tools
+        from . import utopya_tools
 
         # external program:
         prog = "makedepf90"
@@ -2689,7 +2689,7 @@ class UtopyaMake(utopya_rc.UtopyaRc):
         import os
 
         # tools:
-        import utopya_tools
+        from . import utopya_tools
 
         # init base object:
         utopya_rc.UtopyaRc.__init__(self, rcfile=rcfile, rcbase=rcbase, env=env)
diff --git a/src/utopya/utopya_index.py b/src/utopya/utopya_index.py
index cb89cf2..63aa491 100644
--- a/src/utopya/utopya_index.py
+++ b/src/utopya/utopya_index.py
@@ -267,7 +267,7 @@ Classes and methods
 import logging
 
 # tools:
-import utopya
+from . import utopya
 
 
 # -----------------------------------------------------------------------
@@ -925,7 +925,7 @@ class IndexPart(utopya.UtopyaRc):
         """
 
         # tools:
-        import utopya_tools
+        from . import utopya_tools
 
         # read list from settings:
         line = self.GetSetting(key)
diff --git a/src/utopya/utopya_jobscript.py b/src/utopya/utopya_jobscript.py
index dc93201..d2afe2d 100644
--- a/src/utopya/utopya_jobscript.py
+++ b/src/utopya/utopya_jobscript.py
@@ -147,7 +147,7 @@ Classes
 import logging
 
 # tools:
-import utopya_base
+from . import utopya_base
 
 
 # ======================================================================
diff --git a/src/utopya/utopya_jobtree.py b/src/utopya/utopya_jobtree.py
index 7ae1ff2..8c6dbb0 100644
--- a/src/utopya/utopya_jobtree.py
+++ b/src/utopya/utopya_jobtree.py
@@ -105,7 +105,7 @@ Classes
 import logging
 
 # tools:
-import utopya_rc
+from . import utopya_rc
 
 
 # ======================================================================
@@ -470,7 +470,7 @@ class UtopyaJobStep(utopya_rc.UtopyaRc):
         import datetime
 
         # tools:
-        import utopya_tools
+        from . import utopya_tools
 
         # defined ?
         if len(self.logfile) > 0:
@@ -754,7 +754,7 @@ class UtopyaJobStep(utopya_rc.UtopyaRc):
         # add lines to import tools:
         self.Append("")
         self.Append("# tools:")
-        self.Append("import utopya")
+        self.Append("from . import utopya")
         self.Append("")
 
     # enddef AddModules
@@ -3345,7 +3345,7 @@ class UtopyaJobTaskSubmit(UtopyaJobTask):
         import os
 
         # tools:
-        import utopya
+        from . import utopya
 
         # parent init:
         UtopyaJobTask.__init__(self, msg=msg)
@@ -3526,7 +3526,7 @@ class UtopyaRcCommand(utopya_rc.UtopyaRc):
         """
 
         # tools:
-        import utopya_tools
+        from . import utopya_tools
 
         # init base object:
         utopya_rc.UtopyaRc.__init__(self, rcfile=rcfile, rcbase=rcbase, env=env)
@@ -3593,8 +3593,8 @@ class UtopyaJobTreeTiming(utopya_rc.UtopyaRc):
         import os
 
         # tools:
-        import utopya_tools
-        import utopya_timing
+        from . import utopya_tools
+        from . import utopya_timing
 
         # init base object:
         utopya_rc.UtopyaRc.__init__(self, rcfile=rcfile, rcbase=rcbase, env=env)
diff --git a/src/utopya/utopya_post.py b/src/utopya/utopya_post.py
index 0be7490..2c58c62 100644
--- a/src/utopya/utopya_post.py
+++ b/src/utopya/utopya_post.py
@@ -52,7 +52,7 @@ Classes
 import logging
 
 # tools:
-import utopya_base
+from . import utopya_base
 
 
 ############################################################
diff --git a/src/utopya/utopya_rc.py b/src/utopya/utopya_rc.py
index 697c1ba..db5eaf2 100644
--- a/src/utopya/utopya_rc.py
+++ b/src/utopya/utopya_rc.py
@@ -44,7 +44,7 @@ Classes
 import logging
 
 # tools:
-from utopya_base import UtopyaBase
+from .utopya_base import UtopyaBase
 
 
 # -------------------------------------------------
diff --git a/src/utopya/utopya_runscript.py b/src/utopya/utopya_runscript.py
index 8612e74..8782b98 100644
--- a/src/utopya/utopya_runscript.py
+++ b/src/utopya/utopya_runscript.py
@@ -53,8 +53,8 @@ Classes
 import logging
 
 # tools:
-from utopya_base import UtopyaBase
-from utopya_rc import UtopyaRc
+from .utopya_base import UtopyaBase
+from .utopya_rc import UtopyaRc
 
 
 # -------------------------------------------------
-- 
GitLab


From 8c853c43cbefd327b3452e42ec77d50fa33b5a6f Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:26:01 +0000
Subject: [PATCH 11/19] 0.1.dev2

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b48864c..2a3ccec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cso"
-version = "0.1.dev1"
+version = "0.1.dev2"
 authors = [{ name = "Arjo Segers" }]
 description = "CAMS Satellite Operator (CSO) tool."
 readme = "README.md"
-- 
GitLab


From 33c8db32326f39f39ca03235816eb85a0c0459e4 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:30:11 +0000
Subject: [PATCH 12/19] missing one relative import

---
 src/utopya/utopya_rc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/utopya/utopya_rc.py b/src/utopya/utopya_rc.py
index db5eaf2..61c2eb0 100644
--- a/src/utopya/utopya_rc.py
+++ b/src/utopya/utopya_rc.py
@@ -298,7 +298,7 @@ class UtopyaRc(UtopyaBase):
         import sys
 
         # tools:
-        import utopya_tools
+        from . import utopya_tools
 
         # name of model module and class:
         moduleclass = self.GetSetting(name)
-- 
GitLab


From a545d19d722413c151c5a8ce3dc3a744ff05c8ff Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:32:38 +0000
Subject: [PATCH 13/19] fix import in self.Append()

---
 src/utopya/utopya_jobtree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/utopya/utopya_jobtree.py b/src/utopya/utopya_jobtree.py
index 8c6dbb0..cf3f101 100644
--- a/src/utopya/utopya_jobtree.py
+++ b/src/utopya/utopya_jobtree.py
@@ -754,7 +754,7 @@ class UtopyaJobStep(utopya_rc.UtopyaRc):
         # add lines to import tools:
         self.Append("")
         self.Append("# tools:")
-        self.Append("from . import utopya")
+        self.Append("import utopya")
         self.Append("")
 
     # enddef AddModules
-- 
GitLab


From 80ef6fbc31a7e31c68165f45523d5b92b454cc1c Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:34:47 +0000
Subject: [PATCH 14/19] from .cso_dataspace import * in __init__.py

---
 src/cso/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/cso/__init__.py b/src/cso/__init__.py
index 3ce8f6d..85a1b92 100644
--- a/src/cso/__init__.py
+++ b/src/cso/__init__.py
@@ -16,4 +16,5 @@ from .cso_superobs import *
 from .cso_regions import *
 from .cso_constants import *
 from .cso_mapping import *
-from .cso_plot import *
\ No newline at end of file
+from .cso_plot import *
+from .cso_dataspace import *
\ No newline at end of file
-- 
GitLab


From 558b3f1b0db757b80cefa63f487fdeb6f331dda1 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Mon, 14 Apr 2025 13:40:40 +0000
Subject: [PATCH 15/19] pyproject.toml v0.1.0

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2a3ccec..b0e7ae6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cso"
-version = "0.1.dev2"
+version = "0.1.0"
 authors = [{ name = "Arjo Segers" }]
 description = "CAMS Satellite Operator (CSO) tool."
 readme = "README.md"
-- 
GitLab


From 948ed7e8f8af500e488cd9a9e63d8067f08e04f9 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Thu, 24 Apr 2025 07:11:33 +0000
Subject: [PATCH 16/19] Arjo feedback

---
 src/cso/cso_inquire.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/cso/cso_inquire.py b/src/cso/cso_inquire.py
index dc1ecae..c9adcd1 100644
--- a/src/cso/cso_inquire.py
+++ b/src/cso/cso_inquire.py
@@ -226,8 +226,6 @@ class CSO_Inquire_Plot(utopya.UtopyaRc):
                     skip_blank_lines=True,
                     dtype="str",
                 )
-                # convert datetime columns, as the default is "str"
-                # the "parse_dates" argument could not be used:
                 xdf["start_time"] = pandas.to_datetime( xdf["start_time"] )
                 xdf["end_time"] = pandas.to_datetime( xdf["end_time"] )
                 # combine:
-- 
GitLab


From c1539d1b629e2d0a246da4b75f6b5fe3a741581b Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Thu, 24 Apr 2025 07:56:43 +0000
Subject: [PATCH 17/19] resolve conflicts

---
 src/cso/cso_file.py    | 1 -
 src/cso/cso_inquire.py | 1 -
 2 files changed, 2 deletions(-)

diff --git a/src/cso/cso_file.py b/src/cso/cso_file.py
index 2d5ee2d..ee7024d 100644
--- a/src/cso/cso_file.py
+++ b/src/cso/cso_file.py
@@ -1,4 +1,3 @@
-#
 # Changes
 #
 # 2022-09, Arjo Segers
diff --git a/src/cso/cso_inquire.py b/src/cso/cso_inquire.py
index c9adcd1..875d739 100644
--- a/src/cso/cso_inquire.py
+++ b/src/cso/cso_inquire.py
@@ -1,4 +1,3 @@
-#
 # CSO data archive inquiry tools.
 #
 # CHANGES
-- 
GitLab


From e6ebb7c99eb8b67b3736ab1153fac66722073991 Mon Sep 17 00:00:00 2001
From: lewisblake <lewisb@met.no>
Date: Thu, 24 Apr 2025 08:06:04 +0000
Subject: [PATCH 18/19] reresolve conflicts

---
 src/cso/cso_file.py    | 1 +
 src/cso/cso_inquire.py | 1 +
 2 files changed, 2 insertions(+)

diff --git a/src/cso/cso_file.py b/src/cso/cso_file.py
index ee7024d..2d5ee2d 100644
--- a/src/cso/cso_file.py
+++ b/src/cso/cso_file.py
@@ -1,3 +1,4 @@
+#
 # Changes
 #
 # 2022-09, Arjo Segers
diff --git a/src/cso/cso_inquire.py b/src/cso/cso_inquire.py
index 875d739..c9adcd1 100644
--- a/src/cso/cso_inquire.py
+++ b/src/cso/cso_inquire.py
@@ -1,3 +1,4 @@
+#
 # CSO data archive inquiry tools.
 #
 # CHANGES
-- 
GitLab


From e523b6075397921858daa2f7d5350263c76fdd49 Mon Sep 17 00:00:00 2001
From: Lewis Blake <lewisb@met.no>
Date: Thu, 24 Apr 2025 08:10:00 +0000
Subject: [PATCH 19/19] resolve conflicts on web

---
 src/cso/cso_file.py    | 1 -
 src/cso/cso_inquire.py | 1 -
 2 files changed, 2 deletions(-)

diff --git a/src/cso/cso_file.py b/src/cso/cso_file.py
index 2d5ee2d..ee7024d 100644
--- a/src/cso/cso_file.py
+++ b/src/cso/cso_file.py
@@ -1,4 +1,3 @@
-#
 # Changes
 #
 # 2022-09, Arjo Segers
diff --git a/src/cso/cso_inquire.py b/src/cso/cso_inquire.py
index c9adcd1..875d739 100644
--- a/src/cso/cso_inquire.py
+++ b/src/cso/cso_inquire.py
@@ -1,4 +1,3 @@
-#
 # CSO data archive inquiry tools.
 #
 # CHANGES
-- 
GitLab