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Clean up code links
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ahelsing committed Oct 11, 2019
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Expand Up @@ -8,15 +8,15 @@ programs directly specify gates at the physical layer, but with many of the
niceties of a high-level programming language provided by the python host
language.

Documentation on the QGL2 compiler and language, including current known limitations, is in [doc].
Documentation on the QGL2 compiler and language, including current known limitations, is in [doc](doc).

## Examples

For usage examples, see the sample Jupyter notebooks in the [sample notebooks directory](/notebooks).

For code samples, see the [Basic Sequences](/src/python/qgl2/basic_sequences).

For an example of compiling a QGL2 program from the command-line, see [doc/README.txt].
For an example of compiling a QGL2 program from the command-line, see the [docs README](doc/README.txt).

QGL2 directly parses the Python syntax to give natural looking qubit sequences and control flow.
measurement results to variables and control flow statements. For example:
Expand Down Expand Up @@ -112,13 +112,13 @@ def tomo(f, q1: qreg, q2: qreg):
* Install python 3.6; easiest done using [Anaconda](https://www.anaconda.com/distribution/#download-section)
* See below for sample installation given an Anaconda install
* You will need python 3 compatible atom (either atom 1.0.0-dev or ecpy channel atom 0.4)
* Install QGL: (https://github.com/BBN-Q/QGL)
* Install [QGL](https://github.com/BBN-Q/QGL)
* Install QGL dependencies: `cd QGL; pip install -e .`
* From within the QGL git clone, set up git lfs: `<QGL>$ git lfs install`
* Add QGL to your `.bashrc`: `export PYTHONPATH=$QHOME/QGL:$QHOME/pyqgl2/src/python`
* Then: `pip install meta` and `pip install watchdog`
* Optional: `pip install pep8` and `pip install pylint`
* For typical usage, you also need Auspex (https://github.com/BBN-Q/Auspex)
* For typical usage, you also need [Auspex](https://github.com/BBN-Q/Auspex)
* See install instructions at https://auspex.readthedocs.io/en/latest/
* Download or clone, then `cd auspex; pip install -e .`
* Put `Auspex/src` on your `PYTHONPATH` as in above
Expand All @@ -142,14 +142,14 @@ config:

### Dependencies
<!-- Be sure to keep this in sync with .travis.yml and setup.py -->
* Working [https://github.com/BBN-Q/QGL] installation (including `networkx`, `numpy`, `scipy`, `bqplot`, `sqlalchemy`)
* Working [QGL](https://github.com/BBN-Q/QGL) installation (including `networkx`, `numpy`, `scipy`, `bqplot`, `sqlalchemy`)
* Python 3.6
* watchdog and meta
* PYTHONPATH includes `<QGL2 install directory>/src/python`

### Sample install using Anaconda
```bash
<install anaconda python3>
# install anaconda python3
conda install future
conda install -c ecpy atom watchdog
pip install meta
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