From b93e258f2e28a19f84a758b2a99289c10da850f2 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Thu, 27 Oct 2022 09:56:22 -0400 Subject: [PATCH 1/4] :art: Don't display empty `exec` outputs --- docs/_sources/exec.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/docs/_sources/exec.py b/docs/_sources/exec.py index 4da09ccee..e1c32bb0d 100644 --- a/docs/_sources/exec.py +++ b/docs/_sources/exec.py @@ -6,8 +6,8 @@ class ExecDirective(Directive): - """Execute the specified python code and insert the output into the document - """ + """Execute the specified python code and insert the output into the + document""" has_content = True def run(self): @@ -29,7 +29,10 @@ def run(self): try: exec('\n'.join(self.content)) - return [nodes.literal_block(text=sys.stdout.getvalue())] + content = sys.stdout.getvalue() + if content.strip(): + return [nodes.literal_block(text=content)] + return [] except Exception as e: _, _, exc_tb = sys.exc_info() fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1] @@ -39,9 +42,7 @@ def run(self): ) ) stack_message = nodes.paragraph(text=str(e)) - return [ - nodes.error(None, error_message, stack_message) - ] + return [nodes.error(None, error_message, stack_message)] finally: sys.stdout = oldStdout os.chdir(oldCwd) From e7f26de3e5ffe3688c3db6dcf206d2e8e58d60b5 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Thu, 27 Oct 2022 11:04:58 -0400 Subject: [PATCH 2/4] :memo: Add registration submodules to developer docs --- .../developer/workflows/registration.rst | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/docs/_sources/developer/workflows/registration.rst b/docs/_sources/developer/workflows/registration.rst index fc9cd09a0..eebae9dd1 100644 --- a/docs/_sources/developer/workflows/registration.rst +++ b/docs/_sources/developer/workflows/registration.rst @@ -2,5 +2,19 @@ Registration ============ .. automodule:: CPAC.registration - :members: + :members: +.. automodule:: CPAC.registration.exceptions + :members: + +.. automodule:: CPAC.registration.guardrails + :members: + +.. automodule:: CPAC.registration.output_func_to_standard + :members: + +.. automodule:: CPAC.registration.registration + :members: + +.. automodule:: CPAC.registration.utils + :members: From 1a2b1505ed25b2301a0d5bbd1d7a250a77638732 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Thu, 27 Oct 2022 12:12:28 -0400 Subject: [PATCH 3/4] :recycle: Add headers for and resequence registration submodules --- .../developer/workflows/registration.rst | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/docs/_sources/developer/workflows/registration.rst b/docs/_sources/developer/workflows/registration.rst index eebae9dd1..5cbcb5f75 100644 --- a/docs/_sources/developer/workflows/registration.rst +++ b/docs/_sources/developer/workflows/registration.rst @@ -4,17 +4,29 @@ Registration .. automodule:: CPAC.registration :members: +.. automodule:: CPAC.registration.registration + :members: + +Exceptions +^^^^^^^^^^ + .. automodule:: CPAC.registration.exceptions :members: +Guardrails +^^^^^^^^^^ + .. automodule:: CPAC.registration.guardrails :members: +Output_func_to_standard +^^^^^^^^^^^^^^^^^^^^^^^ + .. automodule:: CPAC.registration.output_func_to_standard :members: -.. automodule:: CPAC.registration.registration - :members: +Utils +^^^^^ .. automodule:: CPAC.registration.utils :members: From ce89586a4566dfbbac6cf4ef1be1ddac2f1569c6 Mon Sep 17 00:00:00 2001 From: Jon Clucas Date: Fri, 28 Oct 2022 15:02:50 -0400 Subject: [PATCH 4/4] :memo: Add QC autodocs --- docs/_sources/developer/qc.rst | 23 +++++++++++++++++++++++ docs/_sources/developer/xcpqc.rst | 2 +- docs/_sources/user/pipelines/quality.rst | 2 +- 3 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 docs/_sources/developer/qc.rst diff --git a/docs/_sources/developer/qc.rst b/docs/_sources/developer/qc.rst new file mode 100644 index 000000000..e56cd0944 --- /dev/null +++ b/docs/_sources/developer/qc.rst @@ -0,0 +1,23 @@ +Quality Control +=============== + +.. automodule:: CPAC.qc + :members: + +.. automodule:: CPAC.qc.globals + :members: + +.. automodule:: CPAC.qc.pipeline + :members: + +.. automodule:: CPAC.qc.qc + :members: + +.. automodule:: CPAC.qc.qcmetrics + :members: + +.. automodule:: CPAC.qc.utils + :members: + +.. include:: /developer/xcpqc + diff --git a/docs/_sources/developer/xcpqc.rst b/docs/_sources/developer/xcpqc.rst index d71e94eed..7d36a5341 100644 --- a/docs/_sources/developer/xcpqc.rst +++ b/docs/_sources/developer/xcpqc.rst @@ -1,5 +1,5 @@ eXtensible Connectivity Pipeline-style quality control files -============================================================ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. automodule:: CPAC.qc.xcp :members: diff --git a/docs/_sources/user/pipelines/quality.rst b/docs/_sources/user/pipelines/quality.rst index 40ca146ce..bced83c4f 100644 --- a/docs/_sources/user/pipelines/quality.rst +++ b/docs/_sources/user/pipelines/quality.rst @@ -5,4 +5,4 @@ Quality Control :maxdepth: 1 QC Pages - Visual Data Quality Control - XCP QC files - eXtensible Connectivity Pipeline-style quality control files + Developer Documentation: Quality Control