Fix import errors for docs

Author: inodb

Makefile

@@ -29,10 +29,9 @@ test:
 	nosetests
 
 docs:
-	python doc/add_cli_arguments_to_docs.py
 	$(MAKE) -C doc clean
 	$(MAKE) -C doc html
-	open doc/build/html/index.html
+	open doc/build/html/index.html || see doc/build/html/index.html
 
 release: clean
 	python setup.py sdist upload

doc/add_cli_arguments_to_docs.py

@@ -272,7 +272,7 @@
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
 
-# -- Read the Docs C compilation issues -------------------------------------
+# -- Read the Docs C module import issues -------------------------------------
 
 # See:
 # http://read-the-docs.readthedocs.org/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
@@ -283,6 +283,7 @@ class Mock(MagicMock):
     def __getattr__(cls, name):
             return Mock()
 
-MOCK_MODULES = ['pygtk', 'gtk', 'gobject', 'argparse', 'numpy', 'pandas',
-    'Bio', 'concoct', 'vbgmm', 'concoct.utils']
+MOCK_MODULES = ['pygtk', 'gtk', 'gobject', 'numpy', 'pandas', 'Bio', 'concoct',
+'concoct.utils', 'concoct.output', 'concoct.parser', 'concoct.cluster',
+'concoct.input', 'concoct.transform', 'vbgmm']
 sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)

doc/source/conf.py

@@ -2,16 +2,13 @@
 dnadiff_dist_matrix.py
 ======================
 
-.. command-output:: pwd
-
-Try again
-
 Usage
 =====
 The usage and help documentation of ``dnadiff_dist_matrix.py`` can be seen by
 running ``pyhton dnadiff_dist_matrix -h``:
 
-.. program-output:: python ../../scripts/dnadiff_dist_matrix.py --help
+.. program-output:: (echo 'import conf'; cat ../../scripts/dnadiff_dist_matrix.py) | python - --help
+   :shell:
 
 Example
 =======

doc/source/scripts/dnadiff_dist_matrix.rst

@@ -2,68 +2,9 @@
 Usage
 =====
 
-CONCOCT uses several command line options to control the clustering, here is a complete documentation of these. These can also be viewed by typing ``concoct -h`` on the command line.::
-
-	usage: concoct [-h] [--coverage_file COVERAGE_FILE]
-	               [--composition_file COMPOSITION_FILE] [-c CLUSTERS]
-	               [-k KMER_LENGTH] [-l LENGTH_THRESHOLD] [-r READ_LENGTH]
-	               [--total_percentage_pca TOTAL_PERCENTAGE_PCA] [-b BASENAME]
-	               [-s SEED] [-i ITERATIONS] [-e EPSILON] [--no_cov_normalization]
-	               [--no_total_coverage] [-o] [-d] [-v]
-	
-	optional arguments:
-	  -h, --help            show this help message and exit
-	  --coverage_file COVERAGE_FILE
-	                        specify the coverage file, containing a table where
-	                        each row correspond to a contig, and each column
-	                        correspond to a sample. The values are the average
-	                        coverage for this contig in that sample. All values
-	                        are separated with tabs.
-	  --composition_file COMPOSITION_FILE
-	                        specify the composition file, containing sequences in
-	                        fasta format. It is named the composition file since
-	                        it is used to calculate the kmer composition (the
-	                        genomic signature) of each contig.
-	  -c CLUSTERS, --clusters CLUSTERS
-	                        specify maximal number of clusters for VGMM, default
-	                        400.
-	  -k KMER_LENGTH, --kmer_length KMER_LENGTH
-	                        specify kmer length, default 4.
-	  -l LENGTH_THRESHOLD, --length_threshold LENGTH_THRESHOLD
-	                        specify the sequence length threshold, contigs shorter
-	                        than this value will not be included. Defaults to
-	                        1000.
-	  -r READ_LENGTH, --read_length READ_LENGTH
-	                        specify read length for coverage, default 100
-	  --total_percentage_pca TOTAL_PERCENTAGE_PCA
-	                        The percentage of variance explained by the principal
-	                        components for the combined data.
-	  -b BASENAME, --basename BASENAME
-	                        Specify the basename for files or directory where
-	                        outputwill be placed. Path to existing directory or
-	                        basenamewith a trailing '/' will be interpreted as a
-	                        directory.If not provided, current directory will be
-	                        used.
-	  -s SEED, --seed SEED  Specify an integer to use as seed for clustering. 0
-	                        gives a random seed, 1 is the default seed and any
-	                        other positive integer can be used. Other values give
-	                        ArgumentTypeError.
-	  -i ITERATIONS, --iterations ITERATIONS
-	                        Specify maximum number of iterations for the VBGMM.
-	                        Default value is 500
-	  -e EPSILON, --epsilon EPSILON
-	                        Specify the epsilon for VBGMM. Default value is 1.0e-6
-	  --no_cov_normalization
-	                        By default the coverage is normalized with regards to
-	                        samples, then normalized with regards of contigs and
-	                        finally log transformed. By setting this flag you skip
-	                        the normalization and only do log transorm of the
-	                        coverage.
-	  --no_total_coverage   By default, the total coverage is added as a new
-	                        column in the coverage data matrix, independently of
-	                        coverage normalization but previous to log
-	                        transformation. Use this tag to escape this behaviour.
-	  -o, --converge_out    Write convergence info to files.
-	  -d, --debug           Debug parameters.
-	  -v, --version         show program's version number and exit
+CONCOCT uses several command line options to control the clustering, here is a
+complete documentation of these. These can also be viewed by typing ``concoct
+-h`` on the command line:
 
+.. program-output:: (echo 'import conf'; cat ../../concoct/parser.py; echo 'args=arguments()') | python - --help
+   :shell: