Merge pull request #263 from alneberg/update_doc

Bugfix for the new documentation

doc/requirements.txt

@@ -3,3 +3,4 @@ Sphinx>=1.3.1
 mock>=1.0.1
 sphinxcontrib-programoutput>=0.8
 sphinx-rtd-theme>=0.1.6
+conf

doc/source/cmd_options.rst

@@ -6,5 +6,5 @@ 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:: (concoct -h)
+.. program-output:: (echo 'import conf'; tail -n+2 ../../concoct/parser.py; echo 'args=arguments()') | python - --help
    :shell:

doc/source/conf.py

@@ -299,3 +299,20 @@
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
 #texinfo_no_detailmenu = False
+
+# -- 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
+from mock import Mock as MagicMock
+
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+            return Mock()
+
+MOCK_MODULES = ['pygtk', 'gtk', 'gobject', 'numpy', 'pandas', 'Bio', 'concoct',
+'concoct.utils', 'concoct.output', 'concoct.parser', 'concoct.cluster',
+'concoct.input', 'concoct.transform', 'vbgmm']
+update_d = {mod_name: Mock() for mod_name in MOCK_MODULES}
+sys.modules.update(update_d)

doc/source/scripts/concoct_coverage_table.rst

@@ -1,13 +1,13 @@
-======================
+=========================
 concoct_coverage_table.py
-======================
+=========================
 
 Usage
 =====
 The usage and help documentation of ``concoct_coverage_table.py`` can be seen by
 running ``concoct_coverage_table.py -h``:
 
-.. program-output:: python ../../scripts/concoct_coverage_table.py -h
+.. program-output:: cat ../../scripts/concoct_coverage_table.py | sed 's/import argparse/import argparse, conf/' | python - --help
    :shell:
 
 Example

doc/source/scripts/cut_up_fasta.rst

@@ -7,7 +7,7 @@ Usage
 The usage and help documentation of ``cut_up_fasta.py`` can be seen by
 running ``cut_up_fasta.py -h``:
 
-.. program-output:: python ../../scripts/cut_up_fasta.py -h
+.. program-output:: cat ../../scripts/cut_up_fasta.py | sed 's/import argparse/import argparse, conf/' | python - --help
    :shell:
 
 Example
@@ -19,5 +19,3 @@ An example of how to run ``cut_up_fasta.py``::
 This creates a fasta file and a BED file.
 The fasta file ``contigs_10K.fa`` contains the original contigs cut up into parts of length exactly 10K, except for the last contig part which is between 10K and 20K long.
 The BED file ``contigs_10K.bed`` contains a list of the contig parts created with coordinates in the original contigs.
-
-.. _cut_up_fasta

doc/source/scripts/extract_fasta_bins.rst

@@ -7,7 +7,7 @@ Usage
 The usage and help documentation of ``extract_fasta_bins.py`` can be seen by
 running ``extract_fasta_bins.py -h``:
 
-.. program-output:: python ../../scripts/extract_fasta_bins.py -h
+.. program-output:: cat ../../scripts/extract_fasta_bins.py | sed 's/import argparse/import argparse, conf/' | python - --help
    :shell:
 
 Example

doc/source/scripts/extract_scg_bins.rst

@@ -1,6 +1,6 @@
-======================
+================================
 [Deprecated] extract_scg_bins.py
-======================
+================================
 
 Usage
 =====

doc/source/scripts/merge_cutup_clustering.rst

@@ -1,13 +1,13 @@
-======================
+=========================
 merge_cutup_clustering.py
-======================
+=========================
 
 Usage
 =====
 The usage and help documentation of ``merge_cutup_clustering.py`` can be seen by
 running ``merge_cutup_clustering.py -h``:
 
-.. program-output:: python ../../scripts/merge_cutup_clustering.py -h
+.. program-output:: cat ../../scripts/merge_cutup_clustering.py | sed 's/import argparse/import argparse, conf/' | python - --help
    :shell:
 
 Example