Fixed README with more info on the script, uv

nomad-coe · Jun 6, 2024 · 57be724 · 57be724 · github-actions · Jun 6, 2024
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diff --git a/README.md b/README.md
@@ -21,11 +21,16 @@ python3.9 -m venv .pyenv
 . .pyenv/bin/activate
 ```
 
+We recommend installing `uv` for fast pip installation of the packages:
+```sh
+pip install uv
+```
+
 Install the `nomad-lab` package:
 
 ```sh
 pip install --upgrade pip
-pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+uv pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
 ```
 
 **Note!**
@@ -37,7 +42,7 @@ sure to include NOMAD's internal package registry (via `--index-url` in the abov
 You can run local tests using the `pytest` package:
 
 ```sh
-python -m pytest -sv
+python -m pytest -sv tests
 ```
 
 where the `-s` and `-v` options toggle the output verbosity.
@@ -46,15 +51,20 @@ Our CI/CD pipeline produces a more comprehensive test report using `coverage` an
 
 ```sh
 pip install coverage coveralls
-python -m pytest --cov=src
+python -m pytest --cov=src  tests
+```
+
+You can also run the script to generate a local file `coverage.txt` with the same information by doing:
+```sh
+./scripts/generate_coverage_txt.sh
 ```
 
 ## Development
 
 The plugin is still under development. If you would like to contribute, install the package in editable mode (with the added `-e` flag) with the development dependencies:
 
 ```sh
-pip install -e .[dev] --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+uv pip install -e .[dev] --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
 ```
 
 ### Setting up plugin on your local installation

diff --git a/scripts/generate_coverage_txt.sh b/scripts/generate_coverage_txt.sh
@@ -4,6 +4,4 @@
 python -m pytest --cov=src | tee coverage.txt
 
 # Append the generation message
-echo " " >> coverage.txt
-echo " " >> coverage.txt
-echo -e "\n\nGenerated using './scripts/generate_coverage_txt.sh' in the terminal in the root folder of the project" >> coverage.txt
+echo -e "\n\n\nGenerated using './scripts/generate_coverage_txt.sh' in the terminal in the root folder of the project" >> coverage.txt
File	Stmts	Miss	Cover	Missing
src/nomad_simulations
atoms_state.py	187	18	90%	215–218, 242, 297–298, 366–367, 369, 551, 563–564, 625–629, 644–648, 655
general.py	68	5	93%	84, 148, 258–259, 269
model_method.py	259	74	71%	161–164, 167–174, 265–266, 286, 307–326, 342–368, 371–388, 740, 751, 793–800, 846, 865, 945, 1004, 1079, 1191
model_system.py	257	19	93%	507–510, 558–565, 739–740, 965–969, 975–976, 984–985, 990, 1013
numerical_settings.py	260	62	76%	160, 230, 232–233, 236–239, 243–244, 251–254, 263–266, 270–273, 275–278, 283–286, 292–295, 466–493, 568, 603–606, 630, 633, 678, 680–683, 687, 691, 738, 742–763, 818–819, 886, 895–897, 900
outputs.py	89	6	93%	201–204, 244–247, 272, 274
physical_property.py	90	1	99%	216
variables.py	61	8	87%	110, 133, 153–154, 157, 179, 202, 222
src/nomad_simulations/properties
band_gap.py	48	2	96%	149–150
band_structure.py	107	20	81%	235–267, 280, 287, 323–324, 327
energies.py	21	2	90%	51, 79
fermi_surface.py	12	1	92%	52
hopping_matrix.py	24	2	92%	69, 104
permittivity.py	45	5	89%	110–118
spectral_profile.py	254	123	52%	67–70, 105–108, 209–314, 370–382, 407–410, 430, 435–438, 480–516, 540, 587–590, 606–607, 612–618
src/nomad_simulations/utils
utils.py	66	11	83%	75–84, 93–94, 99, 102
TOTAL	1857	359	81%