docs: update installation instructions to use pixi package manager (#119)

* docs: update installation instructions to use pixi package manager

* docs: update build and upload instructions in CONTRIBUTING.md

* black formatting

* Update readme

Author: melund

CONTRIBUTING.md

@@ -184,8 +184,8 @@ $ rm -fr build
 > 4. Make PR on GitHub, and check docs compile correctly on Github Actions
 > 5. Create a tag with the version number and push it.
 > 6. Crate PYPI pckage
->    : 1. Run `python -m build . --sdist`
->      2. Run `twine upload dist/*`
+>    : 1. Run `pixi run build`
+>      2. Run `pixi run pipy-upload`
 > 7. Update the conda forge package on <https://github.com/conda-forge/anypytools-feedstock>
 
 ## Document History

README.md

@@ -21,14 +21,19 @@ If you use the library for publications please **cite as:**
 
 ## Installation
 
-- Download and install the [Anaconda Python distribution]
-- After installation opens the Anaconda command prompt and type:
+- Download and install the [pixi](https://pixi.sh) package manager
+- After installation open a command prompt in you project directory and type:
 
 ```bash
-conda config --add channels conda-forge
-conda install anypytools
+pixi init
+pixi add anypytools
+pixi install
 ```
 
+This will install a virtual environment with python, anypytools and all
+dependencies. You can then run you scripts in the virtual environment by typing
+by prefixing the command with `pixi run`: e.g. `pixi run python myscript.py`
+
 The library is also available on [PyPi](https://pypi.python.org/pypi/AnyPyTools) for installing using `pip`.
 
 

anypytools/tools.py

@@ -964,6 +964,7 @@ def silentremove(filename):
     except PermissionError as e:
         logging.debug(f"Error removing file: {filename}. Permission denied.")
 
+
 def make_hash(o):
     """Make a hash from a dictionary, list, tuple or set.
 

docs/Tutorial/00_Install_and_setup.ipynb

@@ -12,30 +12,61 @@
     "#### Requirements:\n",
     "\n",
     "* The [AnyBody Modeling System](http://www.anybodytech.com)\n",
-    "* A Scientific Python distribution\n",
+    "* Python\n",
     "\n",
     "\n",
     "#### Easy Installation: \n",
     "\n",
-    "- Download and install the a [conda Python distribution](https://www.continuum.io/downloads)\n",
+    "The best way to get started is using the pixi package manager. It will automatically install python and all needed depencies for you. \n",
     "\n",
-    "- After installation, open the Anaconda command prompt and type:\n",
+    "Install the [pixi](https://pixi.sh/) package manager for Python.\n",
     "\n",
     "> ```bash\n",
-    "> conda config --add channels conda-forge\n",
-    "> conda install anypytools\n",
+    "> powershell -ExecutionPolicy ByPass -c \"irm -useb https://pixi.sh/install.ps1 | ie\n",
     "> ```\n",
-    " \n",
-    "This will install the newest version of AnyPyTools. Note: If Anaconda is 'Installed for all users' it may be necessary to run the command with admin rights. \n",
     "\n",
-    "To update the package in case of newer versions run\n",
+    "After installation, open your working directory in the terminal and run the following command:\n",
     "\n",
-    ">```bash\n",
-    "> conda update anypytools\n",
+    "> ```bash\n",
+    "> pixi init\n",
+    "> pixi add anypytools\n",
+    "> pixi install\n",
     "> ```\n",
+    " \n",
+    "This will create a virtual python environment in that folder and install the AnyPyTools package. Likwise, you can add other depedencies to the virtual environment (e.g. `pixi add jupyter pandas`). All dependencies are tracked in the `pixi.yaml` file which can also be edited manually. \n",
+    "\n",
+    "You can now activate the virtual environment with `pixi shell` and run your scripts. Otherwise, you can prefix your commands with `pixi run` to run them in the virtual environment. \n",
+    "\n",
+    "e.g.: \n",
+    "```bash \n",
+    "pixi run python my_script.py\n",
+    "```\n",
+    "\n",
+    "### Controling the version of AnyBody used by AnyPyTools\n",
+    "\n",
+    "The clever part of using a package manger like pixi is that you can also control which version of the AnyBody console application is used by AnyPyTools.\n",
+    "\n",
+    "A light weight headless version of AnyBody exists as [conda-packages](https://anaconda.org/anybody/anybodycon). Hence, we can install a specific version of AnyBody into our virtual environment. \n",
     "\n",
-    "<img src=\"Tutorial_files/relax.png\" alt=\"\" align=\"left\"  style=\"height: 150px;\"/>"
+    "To do this we first need to add the `anybody` channel to our project. \n",
+    "\n",
+    "```bash\n",
+    "pixi project channel add anybody` \n",
+    "```\n",
+    "\n",
+    "Then we can install a specific version of AnyBody console application. \n",
+    "\n",
+    "```bash\n",
+    "pixi add anybodycon=8.0.4\n",
+    "```\n",
+    "\n",
+    "Now all simulations in this project will use the specified version of AnyBody, regardsless of what is installed on the host system."
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {