Fixed dev setup and install issues for nomad-lab.

.gitlab-ci.yml

@@ -112,6 +112,14 @@ install_tests:
     - pip install `echo dist/nomad-lab-*.tar.gz`[parsing]
     - python -m nomad.cli parse tests/data/parsers/vasp/vasp.xml
 
+dev_setup_tests:
+  stage: test
+  image: python:3.7
+  script:
+    - pip install --upgrade pip
+    - ./setup.sh
+    - python -m nomad.cli parse tests/data/parsers/vasp/vasp.xml
+
 deploy:
   stage: deploy
   before_script:

README.md

@@ -26,12 +26,12 @@ You can install the `nomad` Python package from source distribution with pip. Pl
 note, that this will only install part of NOMAD's dependencies that will only allow
 your to use NOMAD's client library, e.g. to access the NOMAD Archive.
 ```
-pip install nomad --extra-index-url https://repository.nomad-coe.eu/v0.8/dist
+pip install nomad
 ```
 
 To **use the NOMAD parsers for example**, install the `parsing` extra:
 ```
-pip install nomad[parsing] --extra-index-url https://repository.nomad-coe.eu/v0.8/dist
+pip install nomad[parsing]
 nomad parse --show-backend <your-file-to-parse>
 ```
 

dependencies-git.sh

@@ -15,7 +15,9 @@ git config -f .gitmodules --get-regexp '^submodule\..*\.path$' |
             echo "$path is not clean"
             git stash
             git checkout nomad-fair-metainfo
-            git stash apply && git add -A && git commit -a -m "$1"
+            git stash apply
+            git add -A
+            git commit -a -m "$1"
             git push origin nomad-fair-metainfo
         fi
     done

amber @ 56e9412d

-Subproject commit 09b52a7494b9655c53bbe3dcab2719823e5f2e27
+Subproject commit 56e9412d0d322fd88240fe2af41716a0016831c7

asap @ 21f8b2d1

-Subproject commit dd555aad1ce925b5b56be7e55b6650f959ea5261
+Subproject commit 21f8b2d1746685e9dce966c456cab98f044dc8ec

charmm @ 7decbdcf

-Subproject commit dc2b8d5a08fb27e53057f27d9854b22ffee28f06
+Subproject commit 7decbdcf25ef48b019bde17c472f54d65a124c9a

dftbplus @ 0a3e0035

-Subproject commit c447c6b07d8528210975337571c98096caf26770
+Subproject commit 0a3e003535d12b987f5774fc631cb142b6d245c6

fplo @ bb3f0f0d

-Subproject commit e4bd0a1bd72092de4f41c88ebf843265c162a84c
+Subproject commit bb3f0f0daf9714fa4fb861015eb7483fe6b4e750

gromacs @ f7f15620

-Subproject commit ae0068cd75c1b0f6bb818e8cbd5a6a72fe7722f4
+Subproject commit f7f156204c16b54e4df998a8a275bcf4a5aaf901

gromos @ 8d896ede

-Subproject commit 4a74602f7dd287da835cf6a64228b5ad53fd09be
+Subproject commit 8d896ede93e794d0fdb905e42281ef7c871bc05d

lammps @ 9963acbe

-Subproject commit 433f848030759d28bacb780d800877445490da70
+Subproject commit 9963acbe59ab9e8b5b97898aa8f70d9d3ca204c8

mopac @ 2486ca87

-Subproject commit aac03d990b7823776c51a1976b2d5a304e4a1cce
+Subproject commit 2486ca871f6d8f8a189e550c7769e16a5722d697

namd @ 97b653e3

-Subproject commit 3d225e6858fc449e12c5ca45d9597562011f6589
+Subproject commit 97b653e3fe695775f53a96249a0bb9ad694ef742

openkim @ ea31aede

-Subproject commit e38d2615a243c775a378e47a461c731babebf3e6
+Subproject commit ea31aedee7f89cddc3f0bf74dcd79cdbce600949

tinker @ 85cc99b3

-Subproject commit af2bcff3956b83698e3c3fa733df7b5a54264ee1
+Subproject commit 85cc99b320454f8c8a68bdf376e128c156cf2ac2

python_common @ 4c83e96b

-Subproject commit 2e385c1dbf934157d0e533ee709595fd0ccfb742
+Subproject commit 4c83e96bcbf9080d431b7b22f1ecabd4b64dec27

docs/client/install.rst

@@ -5,12 +5,12 @@ We release the NOMAD client library as a Python `distutils <https://docs.python.
 You can download and install it the usual way using *pip* (or *conda*).
 
 Install from pypi
-.. parsed-literal::
+.. code-block:: sh
 
     pip install nomad-lab
 
 Download and install latest release from nomad
-.. parsed-literal::
+.. code-block:: sh
 
     curl https://repository.nomad-coe.eu/v0.8/dist/nomad-lab.tar.gz -o nomad-lab.tar.gz
     pip install ./nomad-lab.tar.gz
@@ -24,14 +24,16 @@ Other functions, e.g. using the NOMAD parsers to parse your code output, require
 additional dependencies. You can use the ``[extra]`` notation to install these extra
 requirements:
 
-.. parsed-literal::
+.. code-block:: sh
 
     pip install nomad-lab[parsing]
     pip install nomad-lab[infrastructure]
     pip install nomad-lab[dev]
+    pip install nomad-lab[all]
 
 The various *extras* have the following meaning:
 
 - ``parsing``, everything necessary to run the parsers
 - ``infrastructure``, everything to run NOMAD services
 - ``dev``, additional tools that are necessary to develop NOMAD
+- ``all``, all of the above

docs/dev/setup.md

@@ -80,7 +80,14 @@ To install libmagick for conda, you can use (other channels might also work):
 conda -c conda-forge install --name nomad_env libmagic
 ```
 
-The next steps can be done using the `setup.sh` script. If you prefere to understand all
+#### pip
+Make sure you have the most recent version of pip:
+```
+pip install --upgrade pip
+```
+
+
+The next steps can be done using the `setup.sh` script. If you prefer to understand all
 the steps and run them manually, read on:
 
 

setup.py

@@ -25,7 +25,7 @@ import fastentrypoints  # pylint: disable=unused-import
 '''
 This setup.py works differently for creating a distribution than installing for
 development. The idea is that for distributions, we compile the requirements, packages, and
-data files from all dependencies and install everything under one package called 'nomad'.
+data files from all dependencies and install everything under one package called 'nomad-lab'.
 For development we install each dependency as its own project. This is mainly due to
 pip's limitation of not being able to install from multiple source folders in develop
 mode.

setup.sh

@@ -3,7 +3,6 @@
 set -e
 
 git submodule sync
-git submodule update --init
-pip install -r requirements.txt
+git submodule update --init --jobs=4
 ./dependencies.sh -e
 pip install -e .
\ No newline at end of file