Merge branch 'main' into adaptive_architecture

Author: huppd

.github/workflows/pre-commit.yml

@@ -19,16 +19,16 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.11.0
+        python-version: 3.10.8
     - uses: conda-incubator/setup-miniconda@v2
       with:
         miniconda-version: "latest"
         channels: conda-forge
         channel-priority: flexible
         show-channel-urls: true
-    - name: Create env from unpinned reqs
+    - name: Create env from pinned environment
       run: |
-        conda env create --name dev_env --file requirements/requirements.yml
+        conda env create --name dev_env --file requirements/environment.yml
     - name: Install pre-commit hooks
       run: |
         conda run --name dev_env pre-commit install-hooks

.github/workflows/pytest.yml

@@ -19,18 +19,18 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.11.0
+        python-version: 3.10.8
     - uses: conda-incubator/setup-miniconda@v2
       with:
         miniconda-version: "latest"
         channels: conda-forge
         channel-priority: flexible
         show-channel-urls: true
-    - name: Create dev env from unpinned reqs
+    - name: Create env from pinned environment
       run: |
-        conda env create --name dev_env --file requirements/requirements.yml
+        ./setup_env.sh -n probtest
     - name: Run Pytest
       env:
         TZ: Europe/Zurich
       run: |
-        conda run --name dev_env pytest -v -s --cov --cov-report=term tests/
+        conda run --name probtest pytest -v -s --cov --cov-report=term tests/

.gitignore

@@ -1,6 +1,5 @@
 .idea*
-.vscode/*
-!.vscode/settings.json
+.vscode
 *pycache*
 *.swp
 *.pdf
@@ -9,6 +8,7 @@
 *.nc
 .coverage
 coverage.xml
+miniconda
 
 # output from unittest
 test_stats.csv

README.md

@@ -80,6 +80,32 @@ Visualize the performance database generated with `performance`.
 
 Even though probtest is used exclusively with ICON at the moment, it does not contain any information about the model or its directory structure. This makes it very flexible and applicable to any circumstance (e.g. usable by Buildbot, Jenkins and human users alike). However, it also requires a lot of information about the model and the data to be processed upon invocation. Since a typical probtest usage involves multiple commands (e.g. run-ensemble -> stats -> tolerance -> check) this leads to a lot of redundancy in the invocation. Therefore, probtest can read commonly used input variables (e.g. the model output directory, the experiment name, the name of the submit script, ...) from a configuration file in json format. To further ease the process, these configuration files can be created from templates using the `init` command. A template for ICON is contained in this repository in the `templates` subdirectory.
 
+### Setup conda
+
+All requirements for using probtest can be easily installed with conda using the
+setup scripts.
+
+For setting up conda you use
+```console
+./setup_miniconda.sh -u
+```
+which will modify your `.bashrc`, or you can use
+```console
+./setup_miniconda.sh
+source miniconda/bin/activate
+```
+which requires to source minconda.
+
+The pinned requirements can be installed by
+```console
+./setup_env.sh
+```
+The unpinned requirements and updating the environment can be done by
+```console
+./setup_env.sh -u -e
+```
+
+
 ### The init command
 
 This command sets up the configuration file. For more help on the command line arguments for `init`, see
@@ -102,13 +128,8 @@ Objective: Run an `exp_name` ICON experiment with an test build and check if the
 output of the test is within a perturbed ensemble of the reference build.
 This is in particular used to validate a GPU build against a CPU reference.
 
-All requirements for using probtest can be easily installed with conda using the
-setup scripts:
-
-```console
-./setup_miniconda.sh
-./setup_env.sh -n probtest -u
-```
+You need to have setup a proper environment, for example as described in the
+section [Setup conda](#setup-conda).
 
 #### Initialize probtest
 Once set up, probtest can generate the config file according to your needs.

engine/cdo_table.py

@@ -45,7 +45,7 @@ def rel_diff_stats(
     horizontal_dims,
     xarray_ds,
     fill_value_key,
-):  # pylint: disable=unused-argument
+):  # pylint: disable=unused-argument, too-many-positional-arguments
     dims = xarray_ds[varname].dims
     dataarray = xarray_ds[varname]
     time = xarray_ds[time_dim].values
@@ -125,7 +125,7 @@ def cdo_table(
     perturbed_model_output_dir,
     cdo_table_file,
     file_specification,
-):
+):  # pylint: disable=too-many-positional-arguments
     # TODO: A single perturbed run provides enough data to make proper statistics.
     #       refactor cdo_table interface to reflect that
     if len(member_num) == 1:

engine/init.py

@@ -96,7 +96,7 @@ def init(
     timing_current,
     timing_reference,
     append_time,
-):
+):  # pylint: disable=too-many-positional-arguments
     template_partition = str(template_name).rpartition("/")
     env = Environment(
         loader=FileSystemLoader(template_partition[0]), undefined=StrictUndefined

engine/performance_check.py

@@ -50,7 +50,7 @@ def performance_check(
     measurement_uncertainty,
     tolerance_factor,
     new_reference_threshold,
-):
+):  # pylint: disable=too-many-positional-arguments
     ttcur = TimingTree.from_json(timing_current)
     ttref = TimingTree.from_json(timing_reference)
 

engine/perturb.py

@@ -100,7 +100,7 @@ def perturb(
     variable_names,
     perturb_amplitude,
     copy_all_files,
-):  # pylint: disable=unused-argument
+):  # pylint: disable=unused-argument, too-many-positional-arguments
 
     processed_member_num = process_member_num(member_num)
 

engine/run_ensemble.py

@@ -71,7 +71,7 @@ def prepare_perturbed_run_script(
     rhs_new,
     rhs_old,
     seed,
-):
+):  # pylint: disable=too-many-positional-arguments
     with open(runscript, "r", encoding="utf-8") as in_file:
         with open(perturbed_runscript, "w", encoding="utf-8") as out_file:
 
@@ -222,7 +222,7 @@ def run_ensemble(
     lhs,
     rhs_new,
     rhs_old,
-):
+):  # pylint: disable=too-many-positional-arguments
     perturbed_run_dir = perturbed_run_dir if perturbed_run_dir else run_dir
     os.chdir(run_dir)
     job_list = []

engine/select_members.py

@@ -33,7 +33,7 @@ def find_members_and_factor_validating_for_all_stats_files(
     min_factor,
     max_factor,
     iterations,
-):
+):  # pylint: disable=too-many-positional-arguments
 
     members = list(range(1, total_member_num + 1))
 
@@ -263,7 +263,7 @@ def select_members(
     min_factor,
     max_factor,
     iterations,
-):  # pylint: disable=unused-argument
+):  # pylint: disable=unused-argument, too-many-positional-arguments
 
     if min_member_num > max_member_num:
         logger.error(