Merge pull request SPARC-X#34 from alchem0x2A/master

Brand renaming

.conda/meta.yaml

@@ -1,4 +1,4 @@
-{% set name = "sparc-dft-api" %}
+{% set name = "SPARC-X-API" %}
 {% set version = "1.0.0" %}
 {% set file_ext = "tar.gz" %}
 {% set readme = load_file_regex(load_file="README.md", regex_pattern=".*")[0] %}
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: python
-  # Install sparc-dft-api and include the psp files
+  # Install and include the psp files
   script: "{{ PYTHON }} -m pip install . --no-deps -vv && cd .. && {{ PYTHON }} -m sparc.download_data"
   entry_points:
     - "sparc-ase = sparc.cli:main"
@@ -33,14 +33,14 @@ requirements:
     - "ase>=3.22"
 
 about:
-  home: https://github.com/SPARC-X/sparc-dft-api
+  home: https://github.com/SPARC-X/{{ name }}
   license: GNU General Public License v3.0
   license_family: GPL3
   license_file: LICENSE
   summary: A Python API for the SPARC DFT Code
   description: {{ readme }}
-  doc_url: https://github.com/SPARC-X/sparc-dft-api/blob/v0.2-alpha/README.md
-  dev_url: https://github.com/SPARC-X/sparc-dft-api
+  doc_url: https://github.com/SPARC-X/{{ name }}/blob/master/README.md
+  dev_url: https://github.com/SPARC-X/{{ name }}
 
 extra:
   recipe-maintainers: Tian Tian ([email protected])

.github/ISSUE_TEMPLATE/bug_report.md

@@ -13,7 +13,7 @@ A concise description of the problem.
 **To Reproduce**
 Provide a minimal list of settings / codes to help us debug, such as
 - Python version
-- Version (git commit hash) of `sparc-dft-api`
+- Version (git commit hash) of `SPARC-X-API`
 - `SPARC` C-code version (see the SPARC .out file header)
 - Your platform and architecture
 

README.md

@@ -1,7 +1,7 @@
 # `SPARC-X-API`: A Python API for the SPARC-X DFT Code
-[![Package](https://raw.githubusercontent.com/alchem0x2A/sparc-dft-api/badges/badges/package.svg)](https://raw.githubusercontent.com/alchem0x2A/sparc-dft-api/badges/badges/package.svg)
-[![Coverage](https://raw.githubusercontent.com/alchem0x2A/sparc-dft-api/badges/badges/coverage.svg)](https://raw.githubusercontent.com/alchem0x2A/sparc-dft-api/badges/badges/coverage.svg)
-[![Unit tests](https://github.com/alchem0x2A/sparc-dft-api/actions/workflows/installation_test.yml/badge.svg)](https://github.com/alchem0x2A/sparc-dft-api/actions/workflows/installation_test.yml)
+[![Package](https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/badges/badges/package.svg)](https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/badges/badges/package.svg)
+[![Coverage](https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/badges/badges/coverage.svg)](https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/badges/badges/coverage.svg)
+[![Unit tests](https://github.com/SPARC-X/SPARC-X-API/actions/workflows/installation_test.yml/badge.svg)](https://github.com/SPARC-X/SPARC-X-API/actions/workflows/installation_test.yml)
 
 `SPARC-X-API` is an [ASE](https://wiki.fysik.dtu.dk/ase/)-compatible Python API for the density functional theory (DFT) code [SPARC](https://github.com/SPARC-X/SPARC). It offers:
 
@@ -23,14 +23,14 @@ which includes the pseudopotential files:
 # Change 'sparc-env' to your desired name if needed
 conda create -n sparc-env
 conda activate sparc-env
-conda install -c alchem0x2a sparc-x-api
+conda install -c alchem0x2a sparc-dft-api
 ```
 
 On Linux platforms (x86_64, aarch64), you can also install the
 precompiled `sparc` DFT binaries alongside the API:
 
 ```bash
-conda install -c alchem0x2a sparc
+conda install -c conda-forge sparc-x
 conda activate sparc-env   # Re-activate to have the env variables effective
 ```
 
@@ -281,7 +281,7 @@ short [MD trajectory](tests/outputs/NH3_sort_lbfgs_opt.sparc).
 
 <img width="1200" alt="image" src="https://github.com/alchem0x2A/SPARC-X-API/assets/6829706/e72329ff-7194-4819-94f8-486ef2218844">
 
-### 5. Units used in `SPARC-X-API`
+### 5. Parameters and units used in `SPARC-X-API`
 
 In the SPARC DFT code, all input parameters conventionally employ atomic units, such as Hartree and Bohr. Conversely, ASE objects (like `Atoms.positions`, `Atoms.cell`, `Atoms.get_potential_energy()`) utilize eV/Angstrom units.
 

doc/advanced_topics.md

@@ -1,5 +1,5 @@
 ## Advanced Topics
-The design of`sparc-dft-api` is schematically shown in the following figure
+The design of `SPARC-X-API` is schematically shown in the following figure
 <img width="929" alt="image" src="https://github.com/alchem0x2A/sparc-dft-api/assets/6829706/3419b1c4-3c56-4fd1-a6de-1ce2aea426e7">
 
 ### Behind the bundle file format
@@ -37,7 +37,7 @@ using only relevant data.
 ### Behind the JSON API
 
 The JSON API are directly parsed from the `SPARC` documentation [LaTeX files](https://github.com/SPARC-X/SPARC/tree/master/doc/.LaTeX). 
-The JSON API file (`sparc/sparc_json_api/parameters.json`) distributed by `sparc-dft-api` is generated by:
+The JSON API file (`sparc/sparc_json_api/parameters.json`) distributed by `SPARC-X-API` is generated by:
 
 ```bash
 git clone https://github.com/SPARC-X/SPARC.git

doc/changes_v0.1.md

@@ -1,6 +1,6 @@
-## Major changes from `sparc-dft-api` [v0.1](https://github.com/SPARC-X/sparc-dft-api/tree/eac557f214b402122a506f88f38c7a8767283503)
+## Major changes from `SPARC-X-API` [v0.1](https://github.com/SPARC-X/SPARC-X-API/tree/eac557f214b402122a506f88f38c7a8767283503)
 
-`sparc-dft-api` has been heavily refactored in v1.0. If you're using legacy Python codes
+`SPARC-X-API` has been heavily refactored in v1.0. If you're using legacy Python codes
 that are written under v0.1 API, there are a few major changes that require your attention:
 
 1. Support for single `.ion` file format is deprecated. Instead, `v0.2` API treats the whole SPARC directory as a bundle format. Please use `read_sparc` and `write_sparc` methods for basic file I/O instead.

doc/contribution_guideline.md

@@ -1,9 +1,9 @@
 ## Submitting issues and pull requests
-We welcome users of SPARC and its python-API to submit issues and pull requests via github.
+We welcome users of SPARC-X and SPARC-X-API to submit issues and pull requests via github.
 When reporting a bug, please make sure to include the following information:
 
-- SPARC version (if available. Should look like "Month Day, Year" in the `.out` file)
-- `sparc-python-api` version or commit hash
+- `SPARC` version (if available. Should look like "Month Day, Year" in the `.out` file)
+- `SPARC-X-API` version or commit hash
 - Minimal example for reproducing the error
 - Error trace message
 
@@ -17,8 +17,8 @@ Pip installation from github's master branch (or your own fork), and download
 a copy of the latest pseudopotential files.
 
 ```python
-git clone https://github.com/SPARC-X/sparc-dft-api.git
-pip install -e "sparc-dft-api[test]"
+git clone https://github.com/SPARC-X/SPARC-X-API.git
+pip install -e "sparc-x-api[test]"
 python -m sparc.download_data
 ```
 
@@ -43,14 +43,14 @@ python -m pytest -svv tests/test_all_dft.py
 ### Adding examples
 
 All examples are listed in `examples/` directory. Please add examples that are important
-for demonstrating the functionalities of `sparc-dft-api` while the calculations can be
+for demonstrating the functionalities of `SPARC-X-API` while the calculations can be
 finished using moderate computating power (e.g. a few minutes with 4 CPU cores).
 
 The examples can have the name in the format `ex[Number]-[purpose].py`.
 
 ### Code structure
 
-Below is a brief overview of the modules in `sparc-dft-api` with simple explanations
+Below is a brief overview of the modules in `SPARC-X-API` with simple explanations
 ```
 sparc
 ├── __init__.py
@@ -95,8 +95,8 @@ Please make sure to exclude any computationally-heavy tests from the step "Test
 
 The CI workflow contains a coverage report step based on the unit test
 and generates a [coverage
-badge](https://github.com/SPARC-X/sparc-dft-api/blob/badges/badges/coverage.svg)
+badge](https://github.com/SPARC-X/SPARC-X-API/blob/badges/badges/coverage.svg)
 on the [`badges`
-branch](https://github.com/SPARC-X/sparc-dft-api/tree/badges).
+branch](https://github.com/SPARC-X/SPARC-X-API/tree/badges).
 
 For repo maintainers, please make sure the `badges` branch is present and **do not merge to this branch**.

doc/troubleshooting.md

@@ -1,5 +1,5 @@
 ### Known issues
-*This is a list of known bugs with the current sparc-dft-api, remove them when PRs are contributed*
+*This is a list of known bugs with the current SPARC-X-API, remove them when PRs are contributed*
 - [ ] `sparc-ase` command currently does not support multi-image yet
 - [ ] `SPARC` calculator may occasionally require more DFT steps than needed during optimization
-- [ ] Raw result parsing from SPARC files may need to be re-factored in a generator form
+- [ ] Raw result parsing from SPARC files may need to be re-factored in a generator form

examples/ex0-eos.py

@@ -1,4 +1,4 @@
-"""A simple example using sparc-dft-api to calculate the equation of state of bulk Al.
+"""A simple example using SPARC-X-API to calculate the equation of state of bulk Al.
 
 Example taken from GPAW's tutorial:
 https://wiki.fysik.dtu.dk/gpaw/tutorialsexercises/structureoptimization/lattice_constants/lattice_constants.html

sparc/calculator.py

@@ -590,7 +590,7 @@ def print_sysinfo(self, command=None):
             command = self.command
         msg = (
             "\n" + "*" * 80 + "\n"
-            f"SPARC program started by sparc-python-api at {now}\n"
+            f"SPARC program started by SPARC-X-API at {now}\n"
             f"command: {command}\n"
         )
         if self.log is None:

sparc/download_data.py

@@ -1,4 +1,4 @@
-"""Download the pseudopotential and other related files after sparc-python-api is installed
+"""Download the pseudopotential and other related files after sparc-x-api is installed
 
 Run:
 

sparc/io.py

@@ -151,7 +151,7 @@ def __find_psp_dir(self, psp_dir=None):
             else:
                 warn(
                     (
-                        "PSP directory bundled with sparc-dft-api is broken! "
+                        "PSP directory bundled with SPARC-X-API is broken! "
                         "Please use `sparc.download_data` to re-download them!"
                     )
                 )

sparc/psp/README.md

@@ -1,4 +1,4 @@
-This is the folder for storing the pseudo potential files with sparc-dft-api. 
+This is the folder for storing the pseudo potential files with SPARC-X-API. 
 During installation, this folder will be intentially kept empty. 
 
 User `python -m sparc.download_data` to download the default pseudo potential files after installation.

sparc/quicktest.py

@@ -140,7 +140,7 @@ def main():
         cprint(
             "\nSome of the tests failed! Please refer to the following resources: \n"
             "1. SPARC's documentation: https://github.com/SPARC-X/SPARC/blob/master/doc/Manual.pdf \n"
-            "2. Python API documentation: https://github.com/SPARC-X/sparc-dft-api/wiki\n",
+            "2. Python API documentation: https://github.com/alchem0x2A/SPARC-X-API/blob/master/README.md\n",
             color="FAIL",
         )
 

sparc/sparc_parsers/aimd.py

@@ -168,4 +168,4 @@ def _write_aimd(
     fileobj,
     data_dict,
 ):
-    raise NotImplementedError("Writing aimd file from python-api " "not supported!")
+    raise NotImplementedError("Writing aimd file from SPARC-X-API " "not supported!")

sparc/sparc_parsers/geopt.py

@@ -134,4 +134,4 @@ def _write_geopt(
     fileobj,
     data_dict,
 ):
-    raise NotImplementedError("Writing geopt file from python-api not supported!")
+    raise NotImplementedError("Writing geopt file from SPARC-X-API not supported!")

sparc/sparc_parsers/out.py

@@ -246,4 +246,4 @@ def _write_out(
     fileobj,
     data_dict,
 ):
-    raise NotImplementedError("Writing output file from python-api not supported!")
+    raise NotImplementedError("Writing output file from SPARC-X-API not supported!")

sparc/sparc_parsers/static.py

@@ -190,4 +190,4 @@ def _write_static(
     fileobj,
     data_dict,
 ):
-    raise NotImplementedError("Writing static file from python-api not supported!")
+    raise NotImplementedError("Writing static file from SPARC-X-API not supported!")

sparc/utils.py

@@ -11,7 +11,7 @@ def deprecated(message):
     def decorator(func):
         def new_func(*args, **kwargs):
             warn(
-                "Function {} is deprecated sparc-dft-api >= v0.2! {}".format(
+                "Function {} is deprecated! {}".format(
                     func.__name__, message
                 ),
                 category=DeprecationWarning,