fix table and install jass_preprocessing in .yml

.gitlab-ci.yml

@@ -15,7 +15,7 @@ pages:
     - pip3 install sphinx
     - pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse
     - pip3 install -r requirements.txt
-    - pip3 install pandas
+    - pip3 install ../jass_preprocessing/
     - cd doc
     - sphinx-apidoc -f -o ./source/_autosummary/ ../jass_preprocessing/
     - make html

doc/source/index.rst

@@ -38,9 +38,9 @@ The QC and preprocessing step goes as follow:
 (input format needed to perform LD-score)
 
 +-------+-----------+--------+----+----+-----+-----+
-| chrom	|    rsID   |  pos   | A0	| A1 |  Z  | P   |
+| chrom	|    rsID   |  pos   | A0 | A1 |  Z  |  P  |
 +-------+-----------+--------+----+----+-----+-----+
-|   1	  | rs4075116	|1003629 | C  | T	 |0.30 | 0.76|
+|   1	| rs4075116	|1003629 | C  | T  | 0.3 | 0.76|
 +-------+-----------+--------+----+----+-----+-----+
 
 
@@ -79,22 +79,22 @@ Input
   * the fields are:
 
 
-+-------------------------------------------+------------------------------------------------------------+
-|                     category              |                         field name                         |
-+===========================================+============================================================+
-|             path to the data              |                            filename                        |
-+-------------------------------------------+------------------------------------------------------------+
-|            study info fields              | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp|
-+-------------------------------------------+------------------------------------------------------------+
-|    names of the header in the GWAS file   |      snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont   |
-+-------------------------------------------+------------------------------------------------------------+
++-------------------------------------------+---------------------------------------------------------------+
+|                     category              |                            field name                         |
++===========================================+===============================================================+
+|             path to the data              |                            filename                           |
++-------------------------------------------+---------------------------------------------------------------+
+|            study info fields              | Consortium,Outcome,fullName,type,Nsample,Ncase,Ncontrol,Nsnp  |
++-------------------------------------------+---------------------------------------------------------------+
+|    names of the header in the GWAS file   |      snpid,a1,a2,freq,pval,n,z,OR,se,code,imp,ncas,ncont      |
++-------------------------------------------+---------------------------------------------------------------+
 
 .. Give an example
 .. |               I don't know                 |                          altNcas,altNcont|
 
 Note that the combination of Consortium and outcome must be unique because it will be used as an index in the cleaning process.
 
-Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na. 
+Here is an example of descriptor field, the field irrelevant (for example odd ratio for continuous trait) for the study must be filled with na.
 
 .. csv-table:: GWAS information table!
 
@@ -117,6 +117,6 @@ Indices and tables
 
 * :ref:`genindex`
 * :ref:`modindex`
-.. automodule:: impute_jass
+.. automodule:: jass_preprocessing
    :members:
 * :ref:`search`