(WIP) documentation improvement.

README.md

@@ -96,7 +96,7 @@ conda install lammps==2019.06.05
 You can specify a different executable name for LAMMPS with:
 
 ```shell
-tox -e py37 -- --lammps-exec lmp_exec
+tox -e 3.9-aiida_lammps -- --lammps-exec lmp_exec
 ```
 
 To output the results of calcjob executions to a specific directory:

docs/source/developers/index.md

@@ -6,31 +6,40 @@ This is a guide for internal development of `aiida-lammps`
 
 The code is formatted and linted using [pre-commit](https://pre-commit.com/), which runs in an isolated, virtual environment:
 
-```shell
-$ pip install pre-commit
-$ pre-commit run --all
+```console
+pip install pre-commit
+pre-commit run --all
 ```
 
 or to automate runs, triggered before each commit:
 
-```shell
-$ pre-commit install
+```console
+pre-commit install
 ```
 
+To avoid problems arising from different configurations in virtual environments, one can also use [tox](https://tox.wiki/en/latest/index.html) to run the pre-commit command inside a clean virtual environment. This can be done in the following manner
+
+```console
+pip install tox
+pip install -e .[pre-commit]
+tox -e pre-commit
+```
+
+
 ## Testing
 
-The test suite can be run in an isolated, virtual environment using `tox` (see `tox.ini` in the repo):
+The test suite can be run in an isolated, virtual environment using `tox` (see `[tool.tox]` in `pyproject.toml`):
 
-```shell
-$ pip install tox
-$ tox -e py37
+```console
+pip install tox
+tox -e 3.8-aiida_lammps
 ```
 
 or directly:
 
-```shell
-$ pip install .[tests]
-$ pytest -v
+```console
+pip install .[tests]
+pytest -v
 ```
 
 The tests require that both PostgreSQL and RabbitMQ are running.
@@ -40,33 +49,33 @@ Some tests require that a `lammps` executable be present.
 
 The easiest way to achieve this is to use Conda:
 
-```shell
-$ conda install lammps==2019.06.05
+```console
+conda install lammps==2019.06.05
 # this will install lmp_serial and lmp_mpi
 ```
 
 You can specify a different executable name for LAMMPS with:
 
-```shell
-$ tox -e py37 -- --lammps-exec lmp_exec
+```console
+tox -e 3.8-aiida_lammps -- --lammps-exec lmp_exec
 ```
 
 To output the results of calcjob executions to a specific directory:
 
-```shell
-$ pytest --lammps-workdir "test_workdir"
+```console
+pytest --lammps-workdir "test_workdir"
 ```
 
 ## Documentation
 
 To run a full docs build:
 
-```shell
-$ tox -e docs-clean
+```console
+tox -e docs-clean
 ```
 
 or to re-build from the current documentation:
 
-```shell
+```console
 $ tox -e docs-update
 ```

docs/source/getting_started/index.md

@@ -29,7 +29,7 @@ The package can be installed either from the Python Package Index {{ PyPI }} or
 :::{tab-item} PyPI
 Installing via {{ PyPI }} can be done making use of the Python package manager {{ pip }}:
 
-```shell
+```console
 pip install aiida-lammps
 ```
 
@@ -39,7 +39,7 @@ This will install the latest release version available in {{ PyPI }}. Other rele
 :::{tab-item} Source
 To install from source one needs to clone the repository and then install the package making use of {{ pip }}:
 
-```shell
+```console
 git clone https://github.com/aiidaplugins/aiida-lammps.git
 pip install -e aiida-lammps
 ```

docs/source/index.md

@@ -38,7 +38,7 @@ reference/api/index
 
 # AiiDA LAMMPS Plugin
 
-{{ aiida_lammps }} is a Python package that allows the workflow management and data provenance tracking framework [AiiDA](http://aiida-core.readthedocs.io/) run {{ LAMMPS }} calculations.
+{{ aiida_lammps }} is a Python package that allows the workflow management and data provenance tracking framework [AiiDA](http://aiida-core.readthedocs.io/) to run {{ LAMMPS }} calculations.
 
 {{ LAMMPS }} is a classical molecular dynamics (MD) code with a focus on materials modeling, it is used broadly inside the MD community due to its flexibility, and in-built capability to generate complex workflows in its input script.
 
@@ -109,6 +109,6 @@ The same basic types of calculations than were previously supported (optimizatio
 
 {{ aiida_lammps }} has been designed in such a way that the base ``Calculation`` method can run a single-phase LAMMPS calculation with as much flexibility as possible, with multi-stage runs being handled by specially designed  ``WorkChains`` instead.
 
-### What does this implies?
+### What does this imply?
 
 Instead of relying on the internal {{ LAMMPS }} scripting language to treat loops, multiple phases, definition of custom variables, etc., those tasks are off loaded to the AiiDA workchains, allowing one to make use of the provenance tracking, automated data storage and caching capabilities of AiiDA.

docs/source/topics/data/potential.md

@@ -1,4 +1,4 @@
-# `LammpsPotentialData`
+# ``LammpsPotentialData``
 
 The potential is one of the most important pieces of data in a MD simulation, since it controls how the atoms interact with each other.
 In ``aiida-lammps`` the potential file is stored in the `LammpsPotentialData` data type, which will store the entire potential file in the database, and add certain attributes so that the data node is easily queryable for later usage. These attributes have been chosen so that they resemble the [OpenKIM](https://openkim.org/doc/schema/kimspec/) standard as much as possible.

docs/source/tutorials/first_md.md

@@ -60,7 +60,7 @@ import requests
 import io
 
 # Download the potential from the repository and store it as a BytesIO object
-_stream = io.BytesIO(requests.get('https://openkim.org/files/MO_546673549085_000/Fe_2.eam.fs').text.encode('ascii'))
+_stream = io.BytesIO(requests.get('https://openkim.org/files/MO_546673549085_000/Fe_2.eam.fs', timeout=20).text.encode('utf-8'))
 
 # Set the metadata for the potential
 potential_parameters = {

docs/source/tutorials/first_raw.md

@@ -90,15 +90,8 @@ As one can notice the script wants to read a file named `data.rhodo` via the [`r
 
 ```python
 import requests
-data = SinglefileData(
-    io.StringIO(
-		textwrap.dedent(
-			requests.get(
-				"https://raw.githubusercontent.com/lammps/lammps/develop/bench/data.rhodo"
-			).text
-		)
-    )
-)
+request = requests.get("https://raw.githubusercontent.com/lammps/lammps/develop/bench/data.rhodo")
+data = SinglefileData(io.StringIO(request.text))
 builder.files = {"data": data}
 builder.filenames = {"data": "data.rhodo"}
 ```

docs/source/tutorials/include/scripts/run_raw_basic.py

@@ -48,16 +48,11 @@
         )
     )
 )
-data = SinglefileData(
-    io.StringIO(
-        textwrap.dedent(
-            requests.get(
-                "https://raw.githubusercontent.com/lammps/lammps/develop/bench/data.rhodo",
-                timeout=20,
-            ).text
-        )
-    )
+request = requests.get(
+    "https://raw.githubusercontent.com/lammps/lammps/develop/bench/data.rhodo",
+    timeout=20,
 )
+data = SinglefileData(io.StringIO(request.text))
 
 builder = CalculationFactory("lammps.raw").get_builder()
 builder.code = load_code("lammps@localhost")

examples/launch_lammps_raw_script.py

@@ -45,16 +45,11 @@
         )
     )
 )
-data = orm.SinglefileData(
-    io.StringIO(
-        textwrap.dedent(
-            requests.get(
-                "https://raw.githubusercontent.com/lammps/lammps/develop/bench/data.rhodo",
-                timeout=20,
-            ).text
-        )
-    )
+request = requests.get(
+    "https://raw.githubusercontent.com/lammps/lammps/develop/bench/data.rhodo",
+    timeout=20,
 )
+data = SinglefileData(io.StringIO(request.text))
 
 builder = plugins.CalculationFactory("lammps.raw").get_builder()
 builder.code = orm.load_code("lammps-23.06.2022@localhost")