update for automatic doc build

.gitlab-ci.yml

 stages:
     - static
+    - dynamic
 
 default:
   tags:
@@ -12,3 +13,25 @@ static-copy:
     script:
         - ls ./Documentation/html/
         - sshpass -p "$WOLKE_PASSWORD" rsync -autv --delete -e "ssh -o StrictHostKeyChecking=no" ./Documentation/html/* "$WOLKE_USER@wolke.img.univie.ac.at:/var/www/flexpart/flexextract"
+
+build:
+    image: harbor.wolke.img.univie.ac.at/podman/flexextract_sphinx:latest
+    stage: dynamic
+    when: manual
+    script:
+        # --strict is too strict :)
+        - cd For_Developers/Sphinx
+        - make html
+    artifacts:
+        paths:
+            - For_Developers/Sphinx/Documentation/html/*
+        expire_in: 60 seconds
+
+deploy:
+  stage: dynamic
+  image: harbor.wolke.img.univie.ac.at/podman/alpine-sshpass:latest
+  when: manual
+  needs:
+    - build
+  script:
+        - sshpass -p "$WOLKE_PASSWORD" rsync -autv --delete -e "ssh -o StrictHostKeyChecking=no" ./For_Developers/Sphinx/Documentation/html/* "$WOLKE_USER@wolke.img.univie.ac.at:/var/www/flexpart/flexextract"

For_developers/Sphinx/Dockerfile

+FROM python:3.7-slim-bullseye
+# install everything
+RUN apt-get update -y \
+ && apt-get install -y -qq texlive texlive-latex-extra pandoc build-essential \
+ && apt-get clean all
+ADD requirements.txt /requirements.txt
+RUN pip install --no-cache -r requirements.txt
+# build the documentation with sphinx?
+#ADD ./Source /doc/Source
+#ADD ./Makefile /doc/Makefile
+WORKDIR /doc
+#RUN make html
\ No newline at end of file

For_developers/Sphinx/Makefile

@@ -6,7 +6,7 @@ SPHINXOPTS    = -d Build_temp
 SPHINXBUILD   = sphinx-build
 SPHINXPROJ    = flex_extract
 SOURCEDIR     = Source
-BUILDDIR      = ../../Documentation
+BUILDDIR      = Documentation
 
 # Put it first so that "make" without argument is like "make help".
 help:

For_developers/Sphinx/Source/_files/CONTROLparameter.xls

-../../../CONTROLparameter.xls
\ No newline at end of file

For_developers/Sphinx/Source/_files/InstallationParameter.xls

-../../../InstallationParameter.xls
\ No newline at end of file

For_developers/Sphinx/Source/_files/SubmitParameters.xls

-../../../SubmitParameters.xls
\ No newline at end of file

For_developers/Sphinx/Source/conf.py

@@ -17,7 +17,6 @@ import sys, glob
 sys.path.insert(0, os.path.abspath('../../../Source/Python'))
 sys.path.insert(0, os.path.abspath('../../../Source/Python/Mods'))
 sys.path.insert(0, os.path.abspath('../../../Source/Python/Classes'))
-
 sys.path.insert(0, os.path.abspath('_static/python'))
 sys.setrecursionlimit(1500)
 

For_developers/Sphinx/requirements.txt

+# using Python 3.7 latest
+# not sure about the version, but sphinx must be version 1.?
+# documentation tool
+sphinx==1.8.5
+sphinx_rtd_theme
+sphinxcontrib-seqdiag
+sphinxcontrib-exceltable
+sphinx-jsonschema
+sphinxcontrib-blockdiag
+seqdiag>=0.9.3,<2
+graphviz
+mock
+pytest
+pylint
+pycallgraph
+Jinja2<3.1
+blockdiag>=1.5.4,<2
\ No newline at end of file

README.md

@@ -2,7 +2,7 @@
 
 `flex_extract` is a software package to support retrieving meteorological fields from the European Centre for Medium-Range Weather Forecasts' (ECMWF) Meteorological Archival and Retrieval System (MARS) as input for the `FLEXTRA`/`FLEXPART` Atmospheric Transport Modelling system.
 
-`FLEXPART` (“FLEXible PARTicle dispersion model”, http://flexpart.eu) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes.
+`FLEXPART` (“FLEXible PARTicle dispersion model”, [flexpart.eu](http://flexpart.eu)) is a Lagrangian transport and dispersion model suitable for the simulation of a large range of atmospheric transport processes.
 
 
 ## Installation and Usage
@@ -12,7 +12,7 @@ Please open the file Documentation/html/index.html in your preferred browser to
 
 ## Project website
 
-https://www.flexpart.eu/wiki/FpInputMetEcmwf
+[flexpart.img.univie.ac.at/flexextract](https://www.flexpart.img.univie.ac.at/flexextract)
 
 ## Authors