DOC: 3.4.0: sphinx warnings `reference target not found`

[kloczek]

First of all currently it is not possible to use straight sphinx-build command to build documentation out of source tree

+ /usr/bin/sphinx-build -n -T -b man docs build/sphinx/man
Running Sphinx v5.1.1

Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 347, in eval_config_file
    exec(code, namespace)
  File "/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/conf.py", line 39, in <module>
    version = release = importlib.metadata.version("pyproj")
  File "/usr/lib64/python3.8/importlib/metadata.py", line 530, in version
    return distribution(distribution_name).version
  File "/usr/lib64/python3.8/importlib/metadata.py", line 503, in distribution
    return Distribution.from_name(distribution_name)
  File "/usr/lib64/python3.8/importlib/metadata.py", line 177, in from_name
    raise PackageNotFoundError(name)
importlib.metadata.PackageNotFoundError: pyproj

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/sphinx/cmd/build.py", line 272, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
  File "/usr/lib/python3.8/site-packages/sphinx/application.py", line 201, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 169, in read
    namespace = eval_config_file(filename, tags)
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 360, in eval_config_file
    raise ConfigError(msg % traceback.format_exc()) from exc
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 347, in eval_config_file
    exec(code, namespace)
  File "/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/conf.py", line 39, in <module>
    version = release = importlib.metadata.version("pyproj")
  File "/usr/lib64/python3.8/importlib/metadata.py", line 530, in version
    return distribution(distribution_name).version
  File "/usr/lib64/python3.8/importlib/metadata.py", line 503, in distribution
    return Distribution.from_name(distribution_name)
  File "/usr/lib64/python3.8/importlib/metadata.py", line 177, in from_name
    raise PackageNotFoundError(name)
importlib.metadata.PackageNotFoundError: pyproj


Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/usr/lib/python3.8/site-packages/sphinx/config.py", line 347, in eval_config_file
    exec(code, namespace)
  File "/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/conf.py", line 39, in <module>
    version = release = importlib.metadata.version("pyproj")
  File "/usr/lib64/python3.8/importlib/metadata.py", line 530, in version
    return distribution(distribution_name).version
  File "/usr/lib64/python3.8/importlib/metadata.py", line 503, in distribution
    return Distribution.from_name(distribution_name)
  File "/usr/lib64/python3.8/importlib/metadata.py", line 177, in from_name
    raise PackageNotFoundError(name)
importlib.metadata.PackageNotFoundError: pyproj

This can be fixed by patch like below:

--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,5 +1,7 @@
 import importlib.metadata
+import sys
 import os
+sys.path.insert(0, os.path.abspath(".."))

 # Sphinx extensions
 extensions = [

This patch fixes what is in the comment and that can of fix is suggested in sphinx example copy.py https://www.sphinx-doc.org/en/master/usage/configuration.html#example-of-configuration-file
This patch allows build documentation without have pyproj module installed ad it guarantees as well that documentation will be generated out of module from source tree and not from installed module (which may be in different version).

Than .. looks like in conf.py is only entry to generate pyproj(1) man page so I've added below patch to generate module documentation as well

--- a/docs/conf.py
+++ b/docs/conf.py
@@ -64,4 +65,19 @@
.
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("cli", "pyproj", "pyproj CLI", [author], 1)]
+man_pages = [
+    (
+        "cli",
+        "pyproj",
+        "pyproj CLI",
+        author,
+        1,
+    ),
+    (
+        "index",
+        "pyproj",
+        "pyproj Python Module Documentation",
+        author,
+        3,
+    )
+]

Than .. on building my packages I'm using sphinx-build command with -n switch which shows warmings about missing references. These are not critical issues.

Here is the output with warnings:

+ /usr/bin/sphinx-build -n -T -b man docs build/sphinx/man
Running Sphinx v5.1.1
making output directory... done
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/docs/objects.inv...
loading intersphinx inventory from https://proj.org/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://shapely.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://docs.xarray.dev/en/stable/objects.inv...
building [mo]: targets for 0 po files that are out of date
building [man]: all manpages
updating environment: [new config] 33 added, 0 changed, 0 removed
reading sources... [100%] transformation_grids
WARNING: autodoc: failed to import class 'aoi.AreaOfInterest' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'aoi.AreaOfUse' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'aoi.BBox' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.CoordinateOperation' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class '_crs.Param' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class '_crs.Grid' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.AlbersEqualAreaConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.AzimuthalEquidistantConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.EquidistantCylindricalConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.GeostationarySatelliteConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.LambertAzimuthalEqualAreaConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.LambertConformalConic1SPConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.LambertConformalConic2SPConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.LambertCylindricalEqualAreaConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.LambertCylindricalEqualAreaScaleConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.MercatorAConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.MercatorBConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.HotineObliqueMercatorBConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.OrthographicConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.PlateCarreeConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.PolarStereographicAConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.PolarStereographicBConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.SinusoidalConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.StereographicConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.UTMConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.TransverseMercatorConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.VerticalPerspectiveConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.RotatedLatitudeLongitudeConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.PoleRotationNetCDFCFConversion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_operation.ToWGS84Transformation' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.CoordinateSystem' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class '_crs.Axis' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_system.Ellipsoidal2DCS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_system.Ellipsoidal3DCS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_system.Cartesian2DCS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.coordinate_system.VerticalCS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.CRS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.GeographicCRS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.DerivedGeographicCRS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.GeocentricCRS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.ProjectedCRS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.VerticalCRS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.BoundCRS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.CompoundCRS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.CustomConstructorCRS' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'crs.is_wkt' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'crs.is_proj' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.Datum' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.datum.CustomDatum' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.Ellipsoid' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.datum.CustomEllipsoid' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.PrimeMeridian' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.datum.CustomPrimeMeridian' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.enums.DatumType' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.enums.CoordinateOperationType' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.enums.Cartesian2DCSAxis' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.enums.Ellipsoidal2DCSAxis' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.enums.Ellipsoidal3DCSAxis' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'crs.enums.VerticalCSAxis' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'database.get_units_map' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'database.Unit' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'database.get_authorities' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'database.get_codes' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'database.query_crs_info' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'database.CRSInfo' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'database.query_utm_crs_info' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'database.get_database_metadata' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'datadir.get_data_dir' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'datadir.set_data_dir' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'datadir.append_data_dir' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'datadir.get_user_data_dir' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'enums.WktVersion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'enums.ProjVersion' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'enums.TransformDirection' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'enums.PJType' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'enums.GeodIntermediateFlag' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import module 'exceptions' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'Geod' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'geod.GeodIntermediateReturn' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'set_use_global_context' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'list.get_proj_operations_map' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'list.get_ellps_map' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'list.get_prime_meridians_map' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'network.set_network_enabled' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'network.is_network_enabled' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'network.set_ca_bundle_path' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'Proj' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'proj.Factors' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'show_versions' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'sync.get_transform_grid_list' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'sync.get_proj_endpoint' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'transformer.Transformer' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import class 'transformer.TransformerGroup' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'transformer.transform' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
WARNING: autodoc: failed to import function 'transformer.itransform' from module 'pyproj'; the following exception was raised:
No module named 'pyproj._network'
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/cli.rst:4: ERROR: Failed to import "parser" from "pyproj.__main__".
No module named 'pyproj._network'
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
writing... pyproj.1 { } python-pyproj.3 { installation examples transformation_grids gotchas api/index api/crs/index api/crs/crs api/crs/coordinate_system api/crs/coordinate_operation api/crs/datum api/crs/enums api/transformer api/geod api/proj api/database api/list api/datadir api/network api/sync api/global_context api/enums api/aoi api/exceptions api/show_versions cli advanced_examples build_crs build_crs_cf crs_compatibility optimize_transformations history past_versions } /home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:14: WARNING: py:class reference target not found: pyproj.crs.CRS
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:19: WARNING: py:class reference target not found: pyproj.crs.CRS
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:130: WARNING: py:class reference target not found: pyproj.crs.CRS
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:236: WARNING: py:class reference target not found: pyproj.crs.CRS
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:285: WARNING: py:class reference target not found: pyproj.transformer.Transformer
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:285: WARNING: py:meth reference target not found: pyproj.crs.CRS.from_user_input
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:285: WARNING: py:class reference target not found: pyproj.transformer.Transformer
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:395: WARNING: py:class reference target not found: pyproj.Geod
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:401: WARNING: py:class reference target not found: pyproj.Geod
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:401: WARNING: py:class reference target not found: pyproj.crs.CRS
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:418: WARNING: py:meth reference target not found: pyproj.Geod.line_length
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:432: WARNING: py:meth reference target not found: pyproj.Geod.geometry_length
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:448: WARNING: py:meth reference target not found: pyproj.Geod.polygon_area_perimeter
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/examples.rst:463: WARNING: py:meth reference target not found: pyproj.Geod.geometry_area_perimeter
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/transformation_grids.rst:88: WARNING: py:obj reference target not found: pyproj.crs.CRS
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/transformation_grids.rst:88: WARNING: py:obj reference target not found: pyproj.Geod
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/transformation_grids.rst:100: WARNING: py:class reference target not found: pyproj.transformer.TransformerGroup
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:73: WARNING: py:class reference target not found: pyproj.Proj
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:73: WARNING: py:class reference target not found: pyproj.transformer.Transformer
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:99: WARNING: py:class reference target not found: pyproj.transformer.Transformer
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:128: WARNING: py:class reference target not found: pyproj.Proj
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:199: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_epsg
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:199: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_authority
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:257: WARNING: py:func reference target not found: pyproj.datadir.get_data_dir
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:258: WARNING: py:func reference target not found: pyproj.datadir.get_data_dir
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:260: WARNING: py:func reference target not found: pyproj.datadir.set_data_dir
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:268: WARNING: py:class reference target not found: pyproj.transformer.Transformer
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:268: WARNING: py:class reference target not found: pyproj.crs.CRS
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:268: WARNING: py:class reference target not found: pyproj.Proj
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:268: WARNING: py:meth reference target not found: pyproj.transformer.transform
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/gotchas.rst:276: WARNING: py:meth reference target not found: pyproj.transformer.transform
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/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:165: WARNING: py:attr reference target not found: pyproj.crs.Ellipsoid.semi_minor_metre
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:173: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_proj4
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/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:194: WARNING: py:func reference target not found: pyproj.get_authorities
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/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:210: WARNING: py:meth reference target not found: pyproj.Geod.polygon_area_perimeter
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:210: WARNING: py:meth reference target not found: pyproj.Geod.line_length
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:210: WARNING: py:meth reference target not found: pyproj.Geod.line_lengths
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:213: WARNING: py:meth reference target not found: pyproj.Geod.geometry_area_perimeter
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:213: WARNING: py:meth reference target not found: pyproj.Geod.geometry_length
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:217: WARNING: py:class reference target not found: pyproj.transformer.TransformerGroup
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:218: WARNING: py:meth reference target not found: pyproj.transformer.Transformer.from_crs
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:218: WARNING: py:meth reference target not found: pyproj.transformer.Transformer.from_proj
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:218: WARNING: py:class reference target not found: pyproj.transformer.TransformerGroup
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:220: WARNING: py:attr reference target not found: pyproj.transformer.Transformer.area_of_use
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:221: WARNING: py:attr reference target not found: pyproj.crs.CoordinateOperation.area_of_use
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:232: WARNING: py:meth reference target not found: pyproj.crs.is_proj
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:233: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_dict
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:233: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_proj4
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:237: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_cf
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:241: WARNING: py:meth reference target not found: pyproj.show_versions
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:254: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_cf
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:254: WARNING: py:meth reference target not found: pyproj.crs.CRS.from_cf
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:256: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_dict
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:257: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_authority
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:258: WARNING: py:attr reference target not found: pyproj.crs.CRS.is_vertical
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:258: WARNING: py:attr reference target not found: pyproj.crs.CRS.is_engineering
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:259: WARNING: py:attr reference target not found: pyproj.crs.CRS.target_crs
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:260: WARNING: py:attr reference target not found: pyproj.crs.CRS.to_wkt
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:261: WARNING: py:attr reference target not found: pyproj.crs.CRS.is_geographic
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:261: WARNING: py:attr reference target not found: pyproj.crs.CRS.is_projected
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:262: WARNING: py:attr reference target not found: pyproj.crs.CRS.is_geocentric
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:263: WARNING: py:meth reference target not found: pyproj.crs.CRS.from_user_input
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:267: WARNING: py:meth reference target not found: pyproj.crs.CRS.to_epsg
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:274: WARNING: py:meth reference target not found: pyproj.transformer.Transformer.transform
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:276: WARNING: py:meth reference target not found: pyproj.transformer.Transformer.to_wkt
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:277: WARNING: py:meth reference target not found: pyproj.transformer.Transformer.from_crs
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:279: WARNING: py:class reference target not found: pyproj.Proj
/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:302: WARNING: py:func reference target not found: pyproj.transformer.transform
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/home/tkloczko/rpmbuild/BUILD/pyproj-3.4.0/docs/history.rst:311: WARNING: py:meth reference target not found: pyproj.transformer.Transformer.from_pipeline
done
build succeeded, 254 warnings.

First part of the warnings about missing pyproj._network module can be skipped because on that stage I have no installed yet pyproj module with its DSOs. However other warningsa are affecting mainly html outpu (I'm interested only man page so I'm not affected)

You can peak on fixes that kind of issues in other projects
latchset/jwcrypto#289
click-contrib/sphinx-click@abc31069
latchset/jwcrypto#289
RDFLib/rdflib-sqlalchemy#95
sissaschool/elementpath@bf869d9e
jaraco/cssutils#21
pywbem/pywbem#2895
sissaschool/xmlschema@42ea98f2
RDFLib/rdflib#2036
frostming/unearth#14
pypa/distlib@98b9b89f

pyproj(1) man page seems is not finished becaue it contains only

PYPROJ(1)                                                                        pyproj                                                                       PYPROJ(1)

NAME
       pyproj - pyproj CLI

AUTHOR
       Jeffrey Whitaker

COPYRIGHT
       2006-2018, Jeffrey Whitaker; 2019-2022, Open source contributors

3.4.0                                                                         Sep 16, 2022                                                                    PYPROJ(1)

[snowman2]

With pyproj installed the man pages look correct man ./pyproj.1:

PYPROJ(1)                           pyproj                           PYPROJ(1)

NAME
       pyproj - pyproj CLI

       pyproj version: 3.4.1.dev0 [PROJ version: 9.1.0]

          usage: pyproj [-h] [-v] {sync} ...

OPTIONS
       -v, --verbose
              Show verbose debugging version information.

              Default: False

SUB-COMMANDS:
   sync
       Tool for synchronizing PROJ datum and transformation support data.

          pyproj sync [-h] [--bbox BBOX] [--spatial-test {intersects,contains}]
                      [--source-id SOURCE_ID] [--area-of-use AREA_OF_USE] [--file FILE]
                      [--exclude-world-coverage] [--include-already-downloaded]
                      [--list-files] [--all] [--system-directory]
                      [--target-directory TARGET_DIRECTORY] [-v]

   options
       --bbox Specify  an  area of interest to restrict the resources to down‐
              load. The area of interest is specified as a bounding  box  with
              geographic  coordinates,  expressed in degrees in an unspecified
              geographic  CRS.  west_long  and  east_long  should  be  in  the
              [-180,180]  range,  and south_lat and north_lat in the [-90,90].
              west_long is generally lower than east_long, except in the  case
              where the area of interest crosses the antimeridian.
...

I am not sure there is a good way to get around not installing pyproj.

I've added below patch to generate module documentation as well

Interesting. I only thought that it would be valuable for the CLI.

[kloczek]

I am not sure there is a good way to get around not installing pyproj.

As on build stage pyproj script does not exist yes maybe it is possible to replace somehow call pyproj.__main__.main? 🤔
As that my patch adds sys.path.insert(0, os.path.abspath("..")) it should be possible to call thet. I'm not sure how to implement that in .rst files ..