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Fix docs build #71

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jeromekelleher opened this issue Aug 22, 2023 · 1 comment
Closed

Fix docs build #71

jeromekelleher opened this issue Aug 22, 2023 · 1 comment
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@daikitag
Milestone
0.0.1 release

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@jeromekelleher
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The docs build is currently failing due to a variety of issues with the source:

/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:4: CRITICAL: Unexpected section title.

Parameters
----------
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:23: CRITICAL: Unexpected section title.

Returns
-------
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:28: CRITICAL: Unexpected section title.

Raises
------
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:35: CRITICAL: Unexpected section title.

See Also
--------
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:40: CRITICAL: Unexpected section title.

Notes
-----
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:65: CRITICAL: Unexpected section title.

Examples
--------
WARNING: autodoc: failed to import class 'TraitModelAdditive' from module 'tstrait'; the following exception was raised:
Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/util/inspect.py", line 380, in safe_getattr
    return getattr(obj, name, *defargs)
AttributeError: module 'tstrait' has no attribute 'TraitModelAdditive'

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

Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/importer.py", line 101, in import_object
    obj = attrgetter(obj, mangled_name)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/__init__.py", line 307, in get_attr
    return autodoc_attrgetter(self.env.app, obj, name, *defargs)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/__init__.py", line 2795, in autodoc_attrgetter
    return safe_getattr(obj, name, *defargs)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/util/inspect.py", line 396, in safe_getattr
    raise AttributeError(name) from exc
AttributeError: TraitModelAdditive

WARNING: autodoc: failed to import class 'TraitModelAlleleFrequency' from module 'tstrait'; the following exception was raised:
Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/util/inspect.py", line 380, in safe_getattr
    return getattr(obj, name, *defargs)
AttributeError: module 'tstrait' has no attribute 'TraitModelAlleleFrequency'

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

Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/importer.py", line 101, in import_object
    obj = attrgetter(obj, mangled_name)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/__init__.py", line 307, in get_attr
    return autodoc_attrgetter(self.env.app, obj, name, *defargs)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/__init__.py", line 2795, in autodoc_attrgetter
    return safe_getattr(obj, name, *defargs)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/util/inspect.py", line 396, in safe_getattr
    raise AttributeError(name) from exc
AttributeError: TraitModelAlleleFrequency

WARNING: autodoc: failed to import class 'Result' from module 'tstrait'; the following exception was raised:
Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/util/inspect.py", line 380, in safe_getattr
    return getattr(obj, name, *defargs)
AttributeError: module 'tstrait' has no attribute 'Result'

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

Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/importer.py", line 101, in import_object
    obj = attrgetter(obj, mangled_name)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/__init__.py", line 307, in get_attr
    return autodoc_attrgetter(self.env.app, obj, name, *defargs)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/__init__.py", line 2795, in autodoc_attrgetter
    return safe_getattr(obj, name, *defargs)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/util/inspect.py", line 396, in safe_getattr
    raise AttributeError(name) from exc
AttributeError: Result

/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.PhenotypeResult:4: CRITICAL: Unexpected section title.

Parameters
----------
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.PhenotypeResult:11: CRITICAL: Unexpected section title.

See Also
--------
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.PhenotypeResult:15: CRITICAL: Unexpected section title.

Examples
--------
WARNING: autodoc: failed to import class 'GenotypeResult' from module 'tstrait'; the following exception was raised:
Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/util/inspect.py", line 380, in safe_getattr
    return getattr(obj, name, *defargs)
AttributeError: module 'tstrait' has no attribute 'GenotypeResult'

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

Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/importer.py", line 101, in import_object
    obj = attrgetter(obj, mangled_name)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/__init__.py", line 307, in get_attr
    return autodoc_attrgetter(self.env.app, obj, name, *defargs)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/ext/autodoc/__init__.py", line 2795, in autodoc_attrgetter
    return safe_getattr(obj, name, *defargs)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/sphinx/util/inspect.py", line 396, in safe_getattr
    raise AttributeError(name) from exc
AttributeError: GenotypeResult

/home/runner/work/tstrait/tstrait/docs/model.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec]
/home/runner/work/tstrait/tstrait/docs/model.md: WARNING: Notebook exception traceback saved in: /home/runner/work/tstrait/tstrait/docs/_build/html/reports/model.err.log [mystnb.exec]
/home/runner/work/tstrait/tstrait/docs/quickstart.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec]
/home/runner/work/tstrait/tstrait/docs/quickstart.md: WARNING: Notebook exception traceback saved in: /home/runner/work/tstrait/tstrait/docs/_build/html/reports/quickstart.err.log [mystnb.exec]
/home/runner/work/tstrait/tstrait/docs/simulation.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec]
/home/runner/work/tstrait/tstrait/docs/simulation.md: WARNING: Notebook exception traceback saved in: /home/runner/work/tstrait/tstrait/docs/_build/html/reports/simulation.err.log [mystnb.exec]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 16%] api                                                   
writing output... [ 33%] installation                                          
writing output... [ 50%] intro                                                 
writing output... [ 66%] model                                                 
writing output... [ 83%] quickstart                                            
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:16: WARNING: undefined label: frequency_dependence
writing output... [100%] simulation                                            
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:41: WARNING: py:class reference target not found: pandas.DataFrame
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:61: WARNING: undefined label: phenotype_model
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.sim_phenotype:66: WARNING: undefined label: quickstart
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.PhenotypeResult:16: WARNING: undefined label: effect_size_output
/home/runner/work/tstrait/tstrait/tstrait/simulate_phenotype.py:docstring of tstrait.simulate_phenotype.PhenotypeResult:16: WARNING: undefined label: phenotype_output
/home/runner/work/tstrait/tstrait/docs/model.md:36: WARNING: py:class reference target not found: TraitModelAdditive
/home/runner/work/tstrait/tstrait/docs/model.md:40: WARNING: py:class reference target not found: TraitModelAdditive
/home/runner/work/tstrait/tstrait/docs/model.md:67: WARNING: py:class reference target not found: TraitModelAlleleFrequency
/home/runner/work/tstrait/tstrait/docs/model.md:79: WARNING: py:class reference target not found: TraitModelAlleleFrequency
/home/runner/work/tstrait/tstrait/docs/model.md:81: WARNING: py:class reference target not found: TraitModelAlleleFrequency
/home/runner/work/tstrait/tstrait/docs/simulation.md:55: WARNING: py:class reference target not found: Result
/home/runner/work/tstrait/tstrait/docs/simulation.md:58: WARNING: py:class reference target not found: GenotypeResult
/home/runner/work/tstrait/tstrait/docs/simulation.md:103: WARNING: py:class reference target not found: GenotypeResult
generating indices... genindex done
highlighting module code... [100%] tstrait.simulate_phenotype                  
writing additional pages... search done
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
[etoc] missing index.html written as redirect to 'intro.html'
build finished with problems, 33 warnings.

===============================================================================

Building your book, returns a non-zero exit code (1). Look above for the cause.

===============================================================================

Error occured; showing saved reports
make: *** [Makefile:8: dev] Error 1
Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
    executenb(
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 1305, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
    return loop.run_until_complete(inner)
  File "/opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
    return future.result()
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 705, in async_execute
    await self.async_execute_cell(
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 1058, in async_execute_cell
    await self._check_raise_for_error(cell, cell_index, exec_reply)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 914, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
import msprime
import tstrait
import matplotlib.pyplot as plt

num_ind = 500
ts = msprime.sim_ancestry(num_ind, sequence_length=1_000_000, recombination_rate=1e-8,
                          population_size=10**4, random_seed=1)
ts = msprime.sim_mutations(ts, rate=1e-8, random_seed=1)

model = tstrait.TraitModelAdditive(trait_mean=0, trait_var=1)
sim_result = tstrait.sim_phenotype(ts, num_causal=1000, model=model, h2=0.3, random_seed=1)

plt.scatter(sim_result.genotype.allele_frequency, sim_result.genotype.effect_size)
plt.xlabel("Allele frequency")
plt.ylabel("Effect size")
plt.axhline(y=0, color='r', linestyle='-')
plt.title("TraitModelAdditive")
plt.show()
------------------


---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[1], line 10
      6 ts = msprime.sim_ancestry(num_ind, sequence_length=1_000_000, recombination_rate=1e-8,
      7                           population_size=10**4, random_seed=1)
      8 ts = msprime.sim_mutations(ts, rate=1e-8, random_seed=1)
---> 10 model = tstrait.TraitModelAdditive(trait_mean=0, trait_var=1)
     11 sim_result = tstrait.sim_phenotype(ts, num_causal=1000, model=model, h2=0.3, random_seed=1)
     13 plt.scatter(sim_result.genotype.allele_frequency, sim_result.genotype.effect_size)

AttributeError: module 'tstrait' has no attribute 'TraitModelAdditive'

Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
    executenb(
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 1305, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
    return loop.run_until_complete(inner)
  File "/opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
    return future.result()
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 705, in async_execute
    await self.async_execute_cell(
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 1058, in async_execute_cell
    await self._check_raise_for_error(cell, cell_index, exec_reply)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 914, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
import msprime
import tstrait
import matplotlib.pyplot as plt

num_ind = 2000
ts = msprime.sim_ancestry(num_ind, sequence_length=1_000_000, recombination_rate=1e-8,
                          population_size=10**4, random_seed=1)
ts = msprime.sim_mutations(ts, rate=1e-8, random_seed=1)

model = tstrait.TraitModelAlleleFrequency(trait_mean=0, trait_var=1, alpha=-0.3)
sim_result = tstrait.sim_phenotype(ts, num_causal=1000, model=model, h2=0.3, random_seed=1)
------------------


---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[1], line 10
      6 ts = msprime.sim_ancestry(num_ind, sequence_length=1_000_000, recombination_rate=1e-8,
      7                           population_size=10**4, random_seed=1)
      8 ts = msprime.sim_mutations(ts, rate=1e-8, random_seed=1)
---> 10 model = tstrait.TraitModelAlleleFrequency(trait_mean=0, trait_var=1, alpha=-0.3)
     11 sim_result = tstrait.sim_phenotype(ts, num_causal=1000, model=model, h2=0.3, random_seed=1)

AttributeError: module 'tstrait' has no attribute 'TraitModelAlleleFrequency'

Traceback (most recent call last):
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
    executenb(
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 1305, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
    return loop.run_until_complete(inner)
  File "/opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
    return future.result()
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 705, in async_execute
    await self.async_execute_cell(
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 1058, in async_execute_cell
    await self._check_raise_for_error(cell, cell_index, exec_reply)
  File "/home/runner/work/tstrait/tstrait/venv/lib/python3.10/site-packages/nbclient/client.py", line 914, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
import msprime
import tstrait

num_ind = 5
ts = msprime.sim_ancestry(num_ind, sequence_length=1_000_000, recombination_rate=1e-8,
                          population_size=10**4, random_seed=1)
ts = msprime.sim_mutations(ts, rate=1e-8, random_seed=1)

model = tstrait.TraitModelAlleleFrequency(trait_mean=0, trait_var=1, alpha=-0.3)
sim_result = tstrait.sim_phenotype(ts, num_causal=3, model=model, h2=0.3, random_seed=1)
------------------


---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[1], line 9
      5 ts = msprime.sim_ancestry(num_ind, sequence_length=1_000_000, recombination_rate=1e-8,
      6                           population_size=10**4, random_seed=1)
      7 ts = msprime.sim_mutations(ts, rate=1e-8, random_seed=1)
----> 9 model = tstrait.TraitModelAlleleFrequency(trait_mean=0, trait_var=1, alpha=-0.3)
     10 sim_result = tstrait.sim_phenotype(ts, num_causal=3, model=model, h2=0.3, random_seed=1)

AttributeError: module 'tstrait' has no attribute 'TraitModelAlleleFrequency'

Error: Process completed with exit code 2.
@jeromekelleher jeromekelleher added this to the 0.0.1 release milestone Aug 22, 2023
@daikitag
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This should be resolved after #77 and #78

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