add auto API docs

doc/source/api.rst

@@ -1,121 +1,18 @@
 API
 ===
 
-This page contains a comprehensive list of all functions within ``pypiper``.
-Docstrings should provide sufficient understanding for any individual function.
 
 pypiper.PipelineManager
 -----------------------
+.. automodule:: pypiper.pypiper
+    :members:
 
-.. currentmodule:: pypiper.pypiper.PipelineManager
-.. autosummary::
-   callprint
-   checkprint
-   clean_add
-   cleanup
-   create_file
-   create_file_racefree
-   exit_handler
-   fail_pipeline
-   ignore_interrupts
-   kill_child_process
-   make_sure_path_exists
-   memory_usage
-   report_command
-   report_profile
-   report_result
-   run
-   set_status_flag
-   signal_int_handler
-   signal_term_handler
-   start_pipeline
-   stop_pipeline
-   time_elapsed
-   timestamp
-   wait_for_lock
-   wait_for_process
 
-pypiper.ngstk
------------------------
-
-.. currentmodule:: pypiper.ngstk.NGSTk
-.. autosummary::
-   addTrackToHub
-   AnnotatePeaks
-   bam2fastq
-   bam_conversions
-   bam_to_fastq
-   bamToBed
-   bamToBigWig
-   bowtie2Map
-   calculateFRiP
-   centerPeaksOnMotifs
-   count_fail_reads
-   count_flag_reads
-   count_lines
-   count_mapped_reads
-   count_multimapping_reads
-   count_reads
-   count_unique_mapped_reads
-   count_unique_reads
-   count_uniquelymapping_reads
-   fastqc
-   fastQC
-   filterPeaksMappability
-   filterReads
-   genomeWideCoverage
-   getFragmentSizes
-   getFRiP
-   getPeakNumber
-   getReadType
-   homerFindMotifs
-   htSeqCount
-   indexBam
-   kallisto
-   linkToTrackHub
-   macs2CallPeaks
-   macs2CallPeaksATACSeq
-   macs2PlotModel
-   make_sure_path_exists
-   makeDir
-   markDuplicates
-   merge_bams
-   mergeBams
-   moveFile
-   parseBowtieStats
-   parseDuplicateStats
-   parseQC
-   peakTools
-   picardMarkDuplicates
-   plotInsertSizesFit
-   preseq_coverage
-   preseq_curve
-   preseq_extrapolate
-   removeDuplicates
-   removeFile
-   sam_conversions
-   samtools_index
-   samtools_view
-   shiftReads
-   skewer
-   slurmFooter
-   slurmHeader
-   slurmSubmitJob
-   sortIndexBam
-   sppCallPeaks
-   topHatMap
-   trimmomatic
-   zinbaCallPeaks
 
-
-Definitions
+pypiper.NGSTk
 -----------------------
 
-.. automodule:: pypiper
-   :members:
-
-.. automodule:: pypiper.pypiper
-   :members:
+.. automodule:: pypiper.ngstk.NGSTk
+    :members:
+.. autosummary::
 
-.. automodule:: pypiper.ngstk
-   :members:

doc/source/conf.py

@@ -18,7 +18,8 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('.'))
+#sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('../../'))
 
 # -- General configuration ------------------------------------------------