Update default profile to be a workflow-profile

Default profile (in `profiles/default`) is now the default workflow profile. Snakemake activates it automatically using the name. This allows the user to inject other profile parameters using the `--profile` cli option. This also allows us to provide the conda configuration as an addition to, rather than a replacement of, the default profile.

Fixes calliope-project#268

docs/workflow/build-remote.md

@@ -1,7 +1,7 @@
 # Build on a cluster
 
 You may want to build the model on a cluster.
-While you can build Euro-Calliope on [any cluster that is supported by Snakemake](https://snakemake.readthedocs.io/en/v6.1.1/executing/cluster.html), our default configuration is targeted at, and tested on, ETH's Euler cluster.
+While you can build Euro-Calliope on [any cluster that is supported by Snakemake](https://snakemake.readthedocs.io/en/v8.10.7/tutorial/additional_features.html#cluster-or-cloud-execution), our default configuration is targeted at, and tested on, ETH's Euler cluster.
 
 ## Build
 
@@ -11,7 +11,7 @@ To build the model on Euler, use the following command:
 snakemake --profile profiles/euler
 ```
 
-If you want to run on another cluster, read [snakemake's documentation on cluster execution](https://snakemake.readthedocs.io/en/stable/executing/cluster.html) and take `profiles/euler` as a starting point.
+If you want to run on another cluster, read [snakemake's documentation on cluster execution](https://snakemake.readthedocs.io/en/v8.10.7/tutorial/additional_features.html#cluster-or-cloud-execution) and take `profiles/euler` as a starting point.
 
 ## Work local, build on remote
 

docs/workflow/customisation.md

@@ -13,19 +13,13 @@ You can, for example, change the temporal and spatial scope of the data and mode
 
 The configuration builds on Snakemake's configuration mechanism and consists of two parts: a default configuration `./config/default.yaml` and a schema declaring all configuration parameters `./config/schema.yaml`.
 To override configuration parameters, you can add another configuration file with just your updates or change parameter values on the command line when calling `snakemake`.
-For details on how the configuration mechanism works, please read [Snakemake's documention](https://snakemake.readthedocs.io/en/v6.1.1/snakefiles/configuration.html).
-
-!!! warning
-    When you change configuration parameters, please consider this important caveat of Snakemake:
-    While Snakemake does understand that parameters have changed, it will not rerun rules with updated parameters by default (see also this [feature request](https://github.com/snakemake/snakemake/issues/976)).
-    To ensure that your configuration parameters are used, you must manually rerun all rules that use the updated parameter.
-    The easiest is to start the build process from scratch by running `snakemake clean`.
+For details on how the configuration mechanism works, please read [Snakemake's documention](https://snakemake.readthedocs.io/en/v8.10.7/snakefiles/configuration.html).
 
 ## Adaptation
 
 Beyond configuration through parameters, you can adapt and extend the workflow in any possible way.
 You can adapt the data pre-processing steps and the way model files are generated, but you can also extend the model by adding your own model files or overrides.
-Customising Euro-Calliope in this way requires a solid understanding of the workflow management system [Snakemake](https://snakemake.readthedocs.io/en/v6.1.1/index.html) that we use.
+Customising Euro-Calliope in this way requires a solid understanding of the workflow management system [Snakemake](https://snakemake.readthedocs.io/en/v8.10.7/index.html) that we use.
 
 Whenever we applied Euro-Calliope in our research we made use of this option.
 Below you will find a list of publications in which we applied Euro-Calliope models.

docs/workflow/overview.md

@@ -2,7 +2,7 @@
 
 Euro-Calliope's workflow builds the models from raw data.
 In essence, it is composed out of three things: scripts that retrieve raw data, process data, and formulate the model; execution environments that explicitly define software dependencies and requirements (equivalent to the conditions in a lab); and the glue ensuring all scripts run in the correct execution environment and the right order.
-Scripts are written in Python; the execution environments are [conda environments](https://docs.conda.io/en/latest/); and the glue holding everything together is the workflow management system [Snakemake](https://snakemake.readthedocs.io/en/v6.1.1/).
+Scripts are written in Python; the execution environments are [conda environments](https://docs.conda.io/en/latest/); and the glue holding everything together is the workflow management system [Snakemake](https://snakemake.readthedocs.io/en/v8.10.7/).
 
 ## Rationale
 

docs/workflow/troubleshooting.md

@@ -7,7 +7,7 @@ running into these problems is completely normal and in many cases a solution is
 Here are some steps we advise you to go through:
 
 1. Read through our frequently asked questions below.
-2. If you did not find an answer to your question, check [Snakemake's documentation](https://snakemake.readthedocs.io/en/v6.1.1/).
+2. If you did not find an answer to your question, check [Snakemake's documentation](https://snakemake.readthedocs.io/en/v8.10.7/).
 3. If you still did not find an answer to your question, [open an issue](https://github.com/calliope-project/euro-calliope/issues/new/choose) on our issue tracker.
 
 ## Frequently Asked Questions

environment.yaml

@@ -6,5 +6,3 @@ dependencies:
     - python=3.11
     - pycountry=18.12.8
     - snakemake-minimal=8.10.7
-variables:
-    SNAKEMAKE_PROFILE: ./profiles/default

profiles/conda/config.yaml

@@ -1,4 +1,3 @@
-software-deployment-method: conda
+# These parameter are considered additional to ./profiles/default/config.yaml.
+# Apply them using the `--profile="profiles/conda` cli option.
 conda-frontend: conda
-cores: 2
-conda-prefix: ../envs/snakemake/euro-calliope/