Repository: ESMValGroup/ESMValCore

Issue:
Version selection does not work if some files are not available for a particular version
Run this script

```python
import logging
from esmvalcore.esgf import find_files

logging.getLogger().setLevel(logging.DEBUG)

if __name__ == '__main__':
    files = find_files(
        dataset='EC-Earth3-Veg',
        project='CMIP6',
        mip='Omon',
        short_name='tos',
        exp='ssp585',
        ensemble='r1i1p1f1',
        grid='gn',
        timerange='2100/2100',
        version='v20200225',
    )
    print("\n".join(str(f) for f in files))
```
results in this stack trace (full output [here](https://github.com/ESMValGroup/ESMValCore/files/11798447/result.txt)):

```
Traceback (most recent call last):
  File "/home/bandela/src/esmvalgroup/esmvalcore/esgf_test.py", line 7, in <module>
    files = find_files(
  File "/home/bandela/src/esmvalgroup/esmvalcore/esmvalcore/esgf/_search.py", line 346, in find_files
    return cached_search(**facets)
  File "/home/bandela/src/esmvalgroup/esmvalcore/esmvalcore/esgf/_search.py", line 360, in cached_search
    files = select_latest_versions(files, facets.get('version'))
  File "/home/bandela/src/esmvalgroup/esmvalcore/esmvalcore/esgf/_search.py", line 67, in select_latest_versions
    raise FileNotFoundError(
FileNotFoundError: Requested versions v20200225 of file not found. Available files: [ESGFFile:CMIP6/ScenarioMIP/EC-Earth-Consortium/EC-Earth3-Veg/ssp585/r1i1p1f1/Omon/tos/gn/v20221112/tos_Omon_EC-Earth3-Veg_ssp585_r1i1p1f1_gn_210101-210112.nc on hosts ['esg-dn1.nsc.liu.se']]
```
The best solution would probably be to not raise an exception but simply skip the files if they are not available for the requested version.


Discussion:

Patch:
diff --git a/conda-linux-64.lock b/conda-linux-64.lock
index 028f61f0f..35c233a4b 100644
--- a/conda-linux-64.lock
+++ b/conda-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 8e2958f9fa6064ce6efdec1ac7b93eb378b7281acae05ab7f6ae326ce198e536
+# input_hash: f879739c343850b4d330edd20df9b167e37702fa57853a23323d74c1ce375b8e
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.5.7-hbcca054_0.conda#f5c65075fc34438d5b456c7f3f5ab695
@@ -27,7 +27,7 @@ https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#
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-https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.8.19-hd590300_0.conda#81bd50906818d08c2f98d6d9f94cbd02
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.8.20-hd590300_0.conda#8717fccceb6a9394d86f37f3b663b4e9
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@@ -36,6 +36,7 @@ https://conda.anaconda.org/conda-forge/linux-64/geos-3.11.2-hcb278e6_0.conda#3b8
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+https://conda.anaconda.org/conda-forge/linux-64/gmp-6.2.1-h58526e2_0.tar.bz2#b94cf2db16066b242ebd26db2facbd56
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@@ -60,7 +61,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.7-h27087fc_0.conda#f
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+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
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@@ -82,10 +83,10 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007
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+https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.5.27-hf85dbcb_0.conda#d067fbf673901a6e0fd323da1eeafe10
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.2.17-h4b87b72_0.conda#183be3df566bc1c143d5d7e0fc60ed8b
+https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.1.10-h4b87b72_0.conda#613b0910286d4feba563ad657ac93372
+https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.1.16-h4b87b72_0.conda#c2a56432ce6009419442dd78e4d63829
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@@ -102,19 +103,18 @@ https://conda.anaconda.org/conda-forge/linux-64/librttopo-1.1.0-h0d5128d_13.cond
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-https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.10.4-hfdac1af_0.conda#241845899caff54ac1d2b3102ad988cf
+https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.11.4-h0d562d8_0.conda#e46fad17d5fb57316b956f88dca765e4
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+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
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+https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.13.26-h0d05201_0.conda#2b8feff4f71c70e9ca0f7ac66b464e8a
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@@ -124,26 +124,27 @@ https://conda.anaconda.org/conda-forge/linux-64/gcc_linux-64-11.4.0-hfd045f2_0.c
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+https://conda.anaconda.org/conda-forge/linux-64/libarchive-3.6.2-h039dbb9_1.conda#29cf970521d30d113f3425b84cb250f6
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diff --git a/environment.yml b/environment.yml
index fbe3cc990..7cbbbef8a 100644
--- a/environment.yml
+++ b/environment.yml
@@ -42,7 +42,7 @@ dependencies:
   - pyyaml
   - requests
   - scipy>=1.6
-  - shapely
+  - shapely >=2.0.0
   - yamale
   # Python packages needed for building docs
   - autodocsumm>=0.2.2
diff --git a/esmvalcore/esgf/_search.py b/esmvalcore/esgf/_search.py
index 76bcfb8c4..87d4cdf09 100644
--- a/esmvalcore/esgf/_search.py
+++ b/esmvalcore/esgf/_search.py
@@ -64,9 +64,8 @@ def select_latest_versions(files, versions):
         if versions:
             selection = [f for f in group if f.facets['version'] in versions]
             if not selection:
-                raise FileNotFoundError(
-                    f"Requested versions {', '.join(versions)} of file not "
-                    f"found. Available files: {group}")
+                # Skip the file if it is not the requested version(s).
+                continue
             group = selection
         latest_version = group[0]
         result.append(latest_version)
diff --git a/esmvalcore/preprocessor/_io.py b/esmvalcore/preprocessor/_io.py
index efdc27d2e..55c80bb1e 100644
--- a/esmvalcore/preprocessor/_io.py
+++ b/esmvalcore/preprocessor/_io.py
@@ -530,7 +530,7 @@ def _concatenate_overlapping_cubes(cubes):
                                     start_overlap.year, start_overlap.month,
                                     start_overlap.day)
             # convert c1_delta scalar cube to vector cube, if needed
-            if c1_delta.data.shape == ():
+            if c1_delta.shape == ():
                 c1_delta = iris.util.new_axis(c1_delta, scalar_coord="time")
             cubes = iris.cube.CubeList([c1_delta, cubes[1]])
             logger.debug("Attempting concatenatenation of %s with %s",
diff --git a/setup.py b/setup.py
index 2073c1817..85273fa39 100755
--- a/setup.py
+++ b/setup.py
@@ -57,7 +57,7 @@ REQUIREMENTS = {
         'requests',
         'scipy>=1.6',
         'scitools-iris>=3.6.0',
-        'shapely',
+        'shapely>=2.0.0',
         'stratify>=0.3',
         'yamale',
     ],


Test patch:
diff --git a/tests/unit/esgf/test_search.py b/tests/unit/esgf/test_search.py
index 52959f2b8..046067cb7 100644
--- a/tests/unit/esgf/test_search.py
+++ b/tests/unit/esgf/test_search.py
@@ -304,8 +304,8 @@ def test_select_latest_versions_filenotfound(mocker):
     file.dataset = 'CMIP6.MODEL.v1'
     file.facets = {'version': 'v1'}
     file.__repr__ = lambda _: 'ESGFFile:CMIP6/MODEL/v1/ta.nc'
-    with pytest.raises(FileNotFoundError):
-        _search.select_latest_versions(files=[file], versions='v2')
+    result = _search.select_latest_versions(files=[file], versions='v2')
+    assert result == []
 
 
 @pytest.mark.parametrize('timerange,selection', [