diff --git a/.github/CHANGELOG.md b/.github/CHANGELOG.md
index e751cf2..b1bc395 100644
--- a/.github/CHANGELOG.md
+++ b/.github/CHANGELOG.md
@@ -5,13 +5,15 @@
* Add partial extended xyz support (https://github.com/briling/v/pull/18)
* Add `j` hotkey to jump to a frame inside and CLI option `frame:%d` to start with a specific frame (https://github.com/briling/v/pull/5)
* Add `bmax` CLI argument for max. bond length (920202b)
-* Python integration (#22, see https://github.com/aligfellow/xyzrender)
+* Add `com` and `exitcom` CLI argument for `gui:0` and on-exit command sequences, respectively
+* Python integration (#28, see https://github.com/aligfellow/xyzrender)
### Improvements
* New colors by @iribirii (https://github.com/briling/v/pull/2, https://github.com/briling/v/pull/13, https://github.com/briling/v/pull/15)
* Remove case sensitivity of xyz file inputs (https://github.com/briling/v/pull/9)
* Add CLI option to disable centering of molecules (https://github.com/briling/v/pull/14)
* Disable default rotation wrt inertia axis for z-matrix input and add a CLI option to force it (https://github.com/briling/v/pull/14)
+* Read molecules from the standard input
### Fixes
* Exit correctly when window closed (https://github.com/briling/v/pull/10)
@@ -19,7 +21,6 @@
* Fix NaNs when compute dihedrals (https://github.com/briling/v/pull/14)
### Still have to be done:
-* documentation for the python bindings
* finish colors (#15)
* ? extended xyz (#16, #17)
* ? fix `readmore` bug (#7)
@@ -27,3 +28,4 @@
* ? how to build on mac
**Full Changelog**: https://github.com/briling/v/compare/v2.0...v3.0rc3
+
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 0000000..7a879df
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,26 @@
+name: Lint Python with Ruff
+
+on:
+ push:
+ branches:
+ - '*'
+ pull_request:
+ branches:
+ - '*'
+
+jobs:
+ lint:
+ if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout code
+ uses: actions/checkout@v5
+ - name: Set up Python
+ uses: actions/setup-python@v5
+ with:
+ python-version: '3.13'
+ - name: Install Ruff
+ run: pip install ruff
+ - name: Run Ruff
+ run: ruff check vmol/ examples/
+ working-directory: ./python
diff --git a/.github/workflows/manual-build.yml b/.github/workflows/manual-build.yml
new file mode 100644
index 0000000..da016eb
--- /dev/null
+++ b/.github/workflows/manual-build.yml
@@ -0,0 +1,8 @@
+name: build
+
+on:
+ workflow_dispatch:
+
+jobs:
+ wheels:
+ uses: ./.github/workflows/wheels.yml
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index cc92dfb..d89a6f4 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -1,6 +1,6 @@
name: release
-on: # triggered by push tagged commits to main
+on: # triggered by push tagged commits
push:
tags:
- 'v*'
@@ -12,44 +12,7 @@ permissions:
jobs:
build_wheels:
- name: Build wheels on ${{ matrix.os }} for python ${{ matrix.py }}
- runs-on: ${{ matrix.os }}
- strategy:
- fail-fast: false
- matrix:
- os: [ubuntu-latest]
- py: ['3.11', '3.12', '3.13']
-
- steps:
-
- - name: install X11 dependencies
- if: ${{ runner.os == 'Linux' }}
- run: |
- sudo apt-get update
- sudo apt install -y libx11-dev libxpm-dev x11proto-dev
-
- - uses: actions/checkout@v6
- with:
- persist-credentials: false
-
- - uses: actions/setup-python@v6
- with:
- python-version: ${{ matrix.py }}
-
- - name: install python
- run: pip install setuptools
-
- - name: build wheels
- working-directory: ./python
- run: python setup.py bdist_wheel
- ## we don't need the wheel name actually, the artifact name just has to be unique
- #run: python setup.py bdist_wheel | grep "creating 'dist" | sed -n "s/^creating 'dist\//WHEEL_NAME='/;s/\s.*$//p" >> "$GITHUB_ENV"
-
- - uses: actions/upload-artifact@v6
- with:
- path: ./python/dist/*.whl
- name: ${{ matrix.os }}.${{ matrix.py }}
-
+ uses: ./.github/workflows/wheels.yml
build_exe:
name: Build the executable file and shared library for ${{ matrix.os }}
@@ -79,6 +42,7 @@ jobs:
./v
./v.so
name: ${{ matrix.os }}.exe
+ if-no-files-found: error
release:
@@ -89,10 +53,6 @@ jobs:
contents: write
steps:
- - name: Check out the repo
- uses: actions/checkout@v6
- with:
- fetch-depth: 0
- uses: actions/download-artifact@v4
with:
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
new file mode 100644
index 0000000..0e6f84f
--- /dev/null
+++ b/.github/workflows/wheels.yml
@@ -0,0 +1,72 @@
+name: Build wheels
+
+on:
+ workflow_call:
+ inputs:
+ package-dir:
+ type: string
+ required: false
+ default: ./python
+ output-dir:
+ type: string
+ required: false
+ default: wheelhouse
+ cibw-build:
+ type: string
+ required: false
+ default: ""
+ cibw-skip:
+ type: string
+ required: false
+ default: "*-musllinux_*"
+ upload-artifact:
+ type: boolean
+ required: false
+ default: true
+
+jobs:
+ build_wheels:
+ name: Build wheels
+ runs-on: ubuntu-latest
+
+ steps:
+
+ - uses: actions/checkout@v6
+ with:
+ fetch-depth: 0
+ persist-credentials: false
+
+ - name: Export git metadata
+ shell: bash
+ run: |
+ set -euo pipefail
+ echo "VMOL_GIT_HASH=${{ github.sha }}" >> "$GITHUB_ENV"
+ echo "VMOL_GIT_BRANCH=${{ github.ref_name }}" >> "$GITHUB_ENV"
+ echo "VMOL_GIT_DESCRIBE=$(git describe --tags --dirty 2>/dev/null || true)" >> "$GITHUB_ENV"
+
+ - uses: actions/setup-python@v6
+ with:
+ python-version: '3.13'
+
+ - name: Install cibuildwheel
+ run: python -m pip install cibuildwheel==3.4.0
+
+ - name: Build wheels
+ run: python -m cibuildwheel "${{ inputs.package-dir }}" --output-dir "${{ inputs.output-dir }}"
+ env:
+ CIBW_BUILD: ${{ inputs.cibw-build }}
+ CIBW_SKIP: ${{ inputs.cibw-skip }}
+ CIBW_BEFORE_ALL_LINUX: |
+ if [ -f /etc/alpine-release ]; then # musllinux (Alpine)
+ apk add --no-cache libx11-dev libxpm-dev pkgconf
+ else # manylinux (AlmaLinux)
+ /usr/bin/dnf -y install libX11-devel libXpm-devel pkgconf-pkg-config
+ fi
+
+ - name: Upload wheels
+ if: ${{ inputs.upload-artifact }}
+ uses: actions/upload-artifact@v6
+ with:
+ name: vmol-wheels-${{ runner.os }}-${{ github.ref_name }}-${{ github.run_number }}
+ path: ${{ inputs.output-dir }}/*.whl
+ if-no-files-found: error
diff --git a/.gitignore b/.gitignore
index 9299e9e..9c6ac0f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,4 @@
vmol.egg-info/
python/build
python/dist
+python/src
diff --git a/README.md b/README.md
index ec840f5..f1d7694 100644
--- a/README.md
+++ b/README.md
@@ -18,6 +18,14 @@ A simple X11 molecular viewer.
- [`.xyz`](https://en.wikipedia.org/wiki/XYZ_file_format) files
- [extended `.xyz`](https://github.com/libAtoms/extxyz) files (currently the extra columns are ignored)
+## Python package (wrapper / API) available
+
+See python package page
+[here.](python/README.md)
+
+Provides wrapper scripts with a simple installation and
+allows to open unsupported file formats with `cclib`.
+
## Download [↑](#download)
```
wget https://github.com/briling/v/releases/download/v2.0/v.2.0 -O v
@@ -40,6 +48,8 @@ make v
```
./v file [file2 ... fileN] [options]
```
+A filename `-` stands for the standard input.
+
Show the reference:
```
./v
@@ -66,8 +76,10 @@ Show the reference:
| `shell:b%lf,%lf` | spheres radii in a.u. |
| `shell:%lf,%lf` | spheres radii in Å |
| `center:%d` | origin is geometric center (`1`, default) / center of mass (`2`) / as is (`0`) |
-| `inertia:1` | rotate molecules wrt axis of inertia |
+| `inertia:%d` | if rotate molecules wrt axis of inertia (`1`) or not (`0`, default) |
| `gui:%d` | normal (default `1`) / headless (`0`) mode |
+| `com:%s` | command sequence for `gui:0` |
+| `exitcom:%s` | command sequence to run on exit (same as for `gui:0`) |
@@ -116,12 +128,20 @@ One can also use the mouse to rotate the molecule and zoom in/out.
Headless mode (in development)
-If run in the headless mode with `gui:0`, the symbols from stdio are processed
+If run in the headless mode with `gui:0`, the symbols from the standard input are processed
as if the corresponding keys were pressed in the normal mode.
-Right now, only `p`, `x`, `z`, and `.` are available. For example,
+Right now, only `p`, `x`, `z`, and `.` are available.
+Command-line option `com:%s` overrides the standard input.
+These examples are equivalent:
```
> echo . | ./v mol/mol0001.xyz gui:0
D*h
+
+> ./v mol/mol0001.xyz gui:0 com:.
+D*h
+
+> cat mol/mol0001.xyz | ./v - gui:0 com:.
+D*h
```