Merge branch 'v0.8.2' into 'master'

0.8.2 release

See merge request !134

.gitlab-ci.yml

@@ -143,19 +143,20 @@ release:
     - docker pull $TEST_IMAGE
     - docker tag $TEST_IMAGE $LATEST_IMAGE
     - docker push $LATEST_IMAGE
-
   except:
     - /^dev-.*$/
   when: manual
+  only:
+    - branches
 
 release_version:
   stage: release
   script:
     - docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN gitlab-registry.mpcdf.mpg.de
-    - docker pull $LATEST_IMAGE
-    - docker tag $LATEST_IMAGE $CI_COMMIT_TAG
-    - docker tag $LATEST_IMAGE $STABLE_IMAGE
+    - docker pull $TEST_IMAGE
+    - docker tag $TEST_IMAGE $LATEST_IMAGE
+    - docker push $LATEST_IMAGE
+    - docker tag $TEST_IMAGE $STABLE_IMAGE
     - docker push $STABLE_IMAGE
-    - docker push $CI_COMMIT_TAG
   only:
     - tags

.gitmodules

-[submodule "dependencies/nomad-meta-info"]
-	path = dependencies/nomad-meta-info
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git
-	branch = nomad-fair
 [submodule "dependencies/python_common"]
 	path = dependencies/python_common
 	url = https://gitlab.mpcdf.mpg.de/nomad-lab/python-common.git
@@ -12,7 +8,7 @@
 	branch = nomad-fair
 [submodule "dependencies/parsers/exciting"]
 	path = dependencies/parsers/exciting
-	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-exciting.git
+	url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-exciting-fairdi.git
 	branch = nomad-fair
 [submodule "dependencies/parsers/fhi-aims"]
 	path = dependencies/parsers/fhi-aims

Dockerfile

@@ -106,26 +106,23 @@ WORKDIR /app
 # transfer installed packages from dependency stage
 COPY --from=build /usr/local/lib/python3.7/site-packages /usr/local/lib/python3.7/site-packages
 RUN echo "copy 1"
-# copy the meta-info, since it files are loaded via relative paths. TODO that should change.
-COPY --from=build /install/dependencies/nomad-meta-info /app/dependencies/nomad-meta-info
-RUN echo "copy 2"
 # copy the documentation, its files will be served by the API
 COPY --from=build /install/docs/.build /app/docs/.build
-RUN echo "copy 3"
+RUN echo "copy 2"
 # copy the source distribution, its files will be served by the API
 COPY --from=build /install/dist /app/dist
-RUN echo "copy 4"
+RUN echo "copy 3"
 # copy the nomad command
 COPY --from=build /usr/local/bin/nomad /usr/bin/nomad
-RUN echo "copy 5"
+RUN echo "copy 4"
 # copy the gui
 RUN mkdir -p /app/gui
 COPY --from=gui_build /app/build /app/gui/build
-RUN echo "copy 6"
+RUN echo "copy 5"
 # copy the encyclopedia gui production code
 COPY --from=gui_build /encyclopedia /app/dependencies/encyclopedia-gui/client
 RUN rm -rf /app/dependencies/encyclopedia-gui/client/src
-RUN echo "copy 7"
+RUN echo "copy 6"
 
 RUN mkdir -p /app/.volumes/fs
 RUN useradd -ms /bin/bash nomad

README.md

@@ -37,7 +37,7 @@ nomad parse --show-backend <your-file-to-parse>
 
 ### For NOMAD developer
 
-Read the [docs](https://repository.nomad-coe.eu/app/docs). The documentation is also part
+Read the [docs](https://repository.nomad-coe.eu/app/docs/index.html). The documentation is also part
 of the source code. It covers aspects like introduction, architecture, development setup/deployment,
 contributing, and API reference.
 

nomad-dos-fingerprints @ 562ae7d2

-Subproject commit bb633623789ee9850873ba0b16a32c66c8265558
+Subproject commit 562ae7d26fa108c7c31ebe38775c767aba1e642c

nomad-meta-info @ a2df84b2

-Subproject commit a2df84b2dfc2c96344e7261580a40d655c904047

aptfim @ d394f7ae

-Subproject commit 45daba83219defb908044193214acce48baf76e9
+Subproject commit d394f7ae375cd2355127abc67e07b1592f18d4f4

eels @ 6f0e7ec8

-Subproject commit 38ed55429bd8c2289471c5dbc162bcdd80b7bb94
+Subproject commit 6f0e7ec897284382d8ef30b0ee0372f010ce468f

exciting @ 0edade50

-Subproject commit 2849061c5212de8e2845ec0c3ed96b7a7f4e67d9
+Subproject commit 0edade50d6be30bc83dca35d382bb6d462ea6f91

fhi-aims @ d342d8a1

-Subproject commit ca7513c0e23b20d738f65b081b482e74a8d0527d
+Subproject commit d342d8a14dc49d528fe7ca867c3f5891d8b73077

mpes @ aa701e8f

-Subproject commit 124b42b9851329682e11c2f1f3e00056d215bd3b
+Subproject commit aa701e8f2780419e7911972c8e2a16d188008902

vasp @ 1a0c8cb0

-Subproject commit ba060d7c8cb902d16e47ca382ef986662a5f3fa4
+Subproject commit 1a0c8cb0801375a78134c67f7a6d31319a338503

python_common @ cf843eda

-Subproject commit 4c83e96bcbf9080d431b7b22f1ecabd4b64dec27
+Subproject commit cf843eda3e4650bc240eb0d1a1ab5b0cea6dda96

docs/api.rst

-API(s) Documentation
+API Reference
 ====================
 
 This is just a brief summary of all API endpoints of the NOMAD API. For a more compelling documention

docs/api_tutorial.md

@@ -69,10 +69,24 @@ identified an entry (given via a `upload_id`/`calc_id`, see the query output), a
 you want to download it:
 
 ```
-curl "http://repository.nomad-coe.eu/app/api/raw/calc/f0KQE2aiSz2KRE47QtoZtw/6xe9fZ9xoxBYZOq5lTt8JMgPa3gX/*" -o download.zip
+curl "http://repository.nomad-coe.eu/app/api/raw/calc/JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z/*" -o download.zip
 ```
 
-This basically requests all the files (`*`) that belong to this entry. If you have a query
+With `*` you basically requests all the files under an entry or path..
+If you need a specific file (that you already know) of that calculation:
+
+```
+curl "http://repository.nomad-coe.eu/app/api/raw/calc/JvdvikbhQp673R4ucwQgiA/k-ckeQ73sflE6GDA80L132VCWp1z/INFO.OUT"
+```
+
+You can also download a specific file from the upload (given a `upload_id`), if you know
+the path of that file:
+
+```
+curl "http://repository.nomad-coe.eu/app/api/raw/JvdvikbhQp673R4ucwQgiA/exciting_basis_set_error_study/monomers_expanded_k8_rgkmax_080_PBE/72_Hf/INFO.OUT"
+```
+
+If you have a query
 that is more selective, you can also download all results. Here all compounds that only
 consist of Si, O, bulk material simulations of cubic systems (currently ~100 entries):
 

docs/archive.rst

 .. _access-the-archive-label:
 
-Accessing the Archive
-=====================
+Using the NOMAD Archive
+=======================
 
 Of course, you can access the NOMAD Archive directly via the NOMAD API (see the `API tutorial <api_tutorial.html>`_
 and `API reference <api.html>`_). But, it is more effective and convenient to use NOMAD's Python client

docs/client/install.rst

@@ -5,14 +5,16 @@ 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
+
 .. code-block:: sh
 
     pip install nomad-lab
 
 Download and install latest release from nomad
+
 .. code-block:: sh
 
-    curl https://repository.nomad-coe.eu/v0.8/dist/nomad-lab.tar.gz -o nomad-lab.tar.gz
+    curl https://repository.nomad-coe.eu/app/dist/nomad-lab.tar.gz -o nomad-lab.tar.gz
     pip install ./nomad-lab.tar.gz
 
 There are different layers of dependencies that you have to install, in order to use

docs/conf.py

@@ -25,8 +25,8 @@ sys.path.insert(0, os.path.abspath('..'))
 
 # -- Project information -----------------------------------------------------
 
-project = 'nomad-FAIRDI'
-copyright = '2018, FAIRDI e.V.'
+project = 'NOMAD Repository and Archive'
+copyright = '2014-2020, FAIRDI e.V.'
 author = 'FAIRDI e.V.'
 
 # The short X.Y version
@@ -200,4 +200,4 @@ def setup(app):
     # }, True)
     # app.add_transform(AutoStructify)
 
-extlinks = {'api': ('https://repository.nomad-coe.eu/v0.8/api/%s', 'NOMAD API ')}
\ No newline at end of file
+extlinks = {'api': ('https://repository.nomad-coe.eu/app/api/%s', 'NOMAD API ')}
\ No newline at end of file