fix snakemake as --cores (-j) is now a mandatory argument

in 5.11.0 https://snakemake.readthedocs.io/en/stable/project_info/history.html

.travis.yml

@@ -19,6 +19,6 @@ before_install:
 
 script:
   - cp ./test/config.test1.yaml ./config.yaml
-  - snakemake solve_all_elec_networks
+  - snakemake -j all solve_all_elec_networks
   - rm -rf resources/*.nc resources/*.geojson resources/*.h5 networks results
   # could repeat for more configurations in future

doc/configuration.rst

@@ -35,7 +35,7 @@ facilitate running multiple scenarios through a single command
 
 .. code:: bash
     
-    snakemake solve_all_elec_networks
+    snakemake -j 1 solve_all_elec_networks
 
 For each wildcard, a **list of values** is provided. The rule ``solve_all_elec_networks`` will trigger the rules for creating ``results/networks/elec_s{simpl}_{clusters}_ec_l{ll}_{opts}.nc`` for **all combinations** of the provided wildcard values as defined by Python's `itertools.product(...) <https://docs.python.org/2/library/itertools.html#itertools.product>`_ function that snakemake's `expand(...) function <https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#targets>`_ uses.
 

doc/introduction.rst

@@ -17,7 +17,7 @@ For instance an invocation to
 
 .. code:: bash
 
-    .../pypsa-eur % snakemake networks/elec_s_128.nc
+    .../pypsa-eur % snakemake -j 1 networks/elec_s_128.nc
 
 follows this dependency graph:
 
@@ -29,7 +29,7 @@ The **blocks** represent the individual rules which are required to create the f
     The dependency graph shown above was generated using
     ``snakemake --dag networks/elec_s_128.nc | dot -Tpng > workflow.png``
 
-For the use of ``snakemake``, it makes sense to familiarize oneself quickly with its `basic tutorial <https://snakemake.readthedocs.io/en/stable/tutorial/basics.html>`_ and then read carefully through the section `Executing Snakemake <https://snakemake.readthedocs.io/en/stable/executable.html>`_, noting the arguments ``-n``, ``-r``, but also ``--dag``, ``-R`` and ``-t``.
+For the use of ``snakemake``, it makes sense to familiarize oneself quickly with its `basic tutorial <https://snakemake.readthedocs.io/en/stable/tutorial/basics.html>`_ and then read carefully through the section `Executing Snakemake <https://snakemake.readthedocs.io/en/stable/executable.html>`_, noting the arguments ``-j``, ``-n``, ``-r``, but also ``--dag``, ``-R`` and ``-t``.
 
 Scenarios, Configuration and Modification
 =========================================

doc/release_notes.rst

@@ -63,7 +63,7 @@ Release Process
 
 * Upload code to `zenodo code repository <https://doi.org/10.5281/zenodo.3520875>`_ with `GNU GPL 3.0 <https://www.gnu.org/licenses/gpl-3.0.en.html>`_ license.
 
-* Create pre-built networks for ``config.default.yaml`` by running ``snakemake extra_components_all_elec_networks``.
+* Create pre-built networks for ``config.default.yaml`` by running ``snakemake -j 1 extra_components_all_elec_networks``.
 
 * Upload pre-built networks to `zenodo data repository <https://doi.org/10.5281/zenodo.3601882>`_ with `CC BY 4.0 <https://creativecommons.org/licenses/by/4.0/>`_ license.
 

doc/tutorial.rst

@@ -103,7 +103,7 @@ clustered down to 6 buses and every 24 hours aggregated to one snapshot. The com
 
 .. code:: bash
 
-    .../pypsa-eur % snakemake results/networks/elec_s_6_ec_lcopt_Co2L-24H.nc
+    .../pypsa-eur % snakemake -j 1 results/networks/elec_s_6_ec_lcopt_Co2L-24H.nc
 
 orders ``snakemake`` to run the script ``solve_network`` that produces the solved network and stores it in ``.../pypsa-eur/results/networks`` with the name ``elec_s_6_ec_lcopt_Co2L-24H.nc``:
 
@@ -120,7 +120,7 @@ orders ``snakemake`` to run the script ``solve_network`` that produces the solve
 .. warning::
     On Windows the previous command may currently cause a ``MissingRuleException`` due to problems with output files in subfolders.
     This is an `open issue <https://github.com/snakemake/snakemake/issues/46>`_ at `snakemake <https://snakemake.readthedocs.io/>`_.
-    Windows users should add the option ``--keep-target-files`` to the command or instead run ``snakemake solve_all_elec_networks``.
+    Windows users should add the option ``--keep-target-files`` to the command or instead run ``snakemake -j 1 solve_all_elec_networks``.
 
 This triggers a workflow of multiple preceding jobs that depend on each rule's inputs and outputs:
     
@@ -242,15 +242,15 @@ You can produce any output file occuring in the ``Snakefile`` by running
 
 .. code:: bash
 
-    .../pypsa-eur % snakemake <output file>
+    .../pypsa-eur % snakemake -j 1 <output file>
 
 For example, you can explore the evolution of the PyPSA networks by running
 
-#. ``.../pypsa-eur % snakemake networks/base.nc``
-#. ``.../pypsa-eur % snakemake networks/elec.nc``
-#. ``.../pypsa-eur % snakemake networks/elec_s.nc``
-#. ``.../pypsa-eur % snakemake networks/elec_s_6.nc``
-#. ``.../pypsa-eur % snakemake networks/elec_s_6_ec_lcopt_Co2L-24H.nc``
+#. ``.../pypsa-eur % snakemake -j 1 networks/base.nc``
+#. ``.../pypsa-eur % snakemake -j 1 networks/elec.nc``
+#. ``.../pypsa-eur % snakemake -j 1 networks/elec_s.nc``
+#. ``.../pypsa-eur % snakemake -j 1 networks/elec_s_6.nc``
+#. ``.../pypsa-eur % snakemake -j 1 networks/elec_s_6_ec_lcopt_Co2L-24H.nc``
 
 There's a special rule: If you simply run
 

doc/wildcards.rst

@@ -124,7 +124,7 @@ in Germany (in the solution for Europe) use:
 
 .. code:: bash
 
-    snakemake results/summaries/elec_s_all_lall_Co2L-3H_DE
+    snakemake -j 1 results/summaries/elec_s_all_lall_Co2L-3H_DE
 
 .. seealso::
     :mod:`make_summary`, :mod:`plot_summary`, :mod:`plot_p_nom_max`