From 7e60941dced9b16c41adb864651523a1df5e9da3 Mon Sep 17 00:00:00 2001
From: Bouwe Andela <b.andela@esciencecenter.nl>
Date: Wed, 20 Dec 2023 10:31:50 +0100
Subject: [PATCH] Update dependencies (#3487)

---
 environment.yml     | 10 +++++-----
 environment_osx.yml | 11 ++++++-----
 setup.py            | 15 ++++++++-------
 3 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/environment.yml b/environment.yml
index 6409a35e6a..660cd7f11e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,8 +9,6 @@ channels:
   - nodefaults
 
 dependencies:
-  - pip !=21.3
-  - python >=3.9
   - aiohttp
   - cartopy
   - cdo >=1.9.7
@@ -28,7 +26,7 @@ dependencies:
   - fiona
   - fire
   - gdal
-  - iris >=3.6.0
+  - iris >=3.6.1
   - iris-esmf-regrid >=0.7.0
   - jinja2
   - joblib
@@ -40,9 +38,10 @@ dependencies:
   - netCDF4
   - numba
   - numpy !=1.24.3  # severe masking bug
-  - packaging
   - openpyxl
+  - packaging
   - pandas
+  - pip !=21.3
   - progressbar2
   - prov
   - psyplot
@@ -50,6 +49,7 @@ dependencies:
   - psy-reg
   - psy-simple
   - pyproj >=2.1
+  - python >=3.9
   - python-cdo
   - python-dateutil
   - pyyaml
@@ -61,7 +61,7 @@ dependencies:
   - scipy
   - seaborn
   - seawater
-  - shapely
+  - shapely >=2
   - xarray >=0.12.0
   - xesmf >=0.7.1
   - xgboost >1.6.1  # github.com/ESMValGroup/ESMValTool/issues/2779
diff --git a/environment_osx.yml b/environment_osx.yml
index 7207ec9112..0d1f034e61 100644
--- a/environment_osx.yml
+++ b/environment_osx.yml
@@ -9,8 +9,6 @@ channels:
   - nodefaults
 
 dependencies:
-  - pip !=21.3
-  - python >=3.9
   - aiohttp
   - cartopy
   - cdo >=1.9.7
@@ -28,7 +26,7 @@ dependencies:
   - fiona
   - fire
   - gdal
-  - iris >=3.6.0
+  - iris >=3.6.1
   - iris-esmf-regrid >=0.7.0
   - jinja2
   - joblib
@@ -38,10 +36,12 @@ dependencies:
   - natsort
   - nc-time-axis
   - netCDF4
+  - numba
   - numpy !=1.24.3  # severe masking bug
-  - packaging
   - openpyxl
+  - packaging
   - pandas
+  - pip !=21.3
   - progressbar2
   - prov
   - psyplot
@@ -49,6 +49,7 @@ dependencies:
   - psy-reg
   - psy-simple
   - pyproj>=2.1
+  - python >=3.9
   - python-cdo
   - python-dateutil
   - pyyaml
@@ -60,7 +61,7 @@ dependencies:
   - scipy
   - seaborn
   - seawater
-  - shapely
+  - shapely >=2
   - xarray >=0.12.0
   - xesmf >=0.7.1
   - xgboost >1.6.1  # github.com/ESMValGroup/ESMValTool/issues/2779
diff --git a/setup.py b/setup.py
index bd584b7b3b..34ef66d80e 100755
--- a/setup.py
+++ b/setup.py
@@ -35,6 +35,7 @@
         'esmvalcore',
         'esmf-regrid>=0.7.0',
         'fiona',
+        'fire',
         'GDAL',
         'jinja2',
         'joblib',
@@ -46,27 +47,27 @@
         'netCDF4',
         'numba',
         'numpy!=1.24.3',  # severe masking bug
-        'packaging',
         'openpyxl',
+        'packaging',
         'pandas',
-        'pyproj>=2.1',
-        'pyyaml',
         'progressbar2',
         'psyplot',
         'psy-maps',
         'psy-reg',
         'psy-simple',
+        'pyproj>=2.1',
+        'python-dateutil',
+        'pyyaml',
         'rasterio',
+        'requests',
         'ruamel.yaml',
         'scikit-image',
         'scikit-learn',
         'scipy',
-        # See the following issue for info on the iris pin below:
-        # https://github.com/ESMValGroup/ESMValTool/issues/3239#issuecomment-1613298587
-        'scitools-iris>=3.4.0',
+        'scitools-iris>=3.6.1',
         'seaborn',
         'seawater',
-        'shapely',
+        'shapely>=2',
         'xarray>=0.12.0',
         'xesmf>=0.7.1',
         'xgboost>1.6.1',  # github.com/ESMValGroup/ESMValTool/issues/2779