README.md 7.43 KB
Newer Older
Markus Scheidgen's avatar
Markus Scheidgen committed
1
2
3
[![pipeline status](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/badges/master/pipeline.svg)](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/commits/master)
[![coverage report](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/badges/master/coverage.svg)](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/commits/master)

4
5
6
7
This project implements the new *nomad@FAIRDI* infrastructure. Contrary to its NOMAD CoE
predecessor, it implements the NOMAD Repository and NOMAD Archive functionality within
a single cohesive application. This project provides all necessary artifacts to develop,
test, deploy, and operate the NOMAD Respository and Archive, e.g. at
8
[https://nomad-lab.eu](https://nomad-lab.eu).
9
10
11
12

In the future, this project's aim is to integrate more NOMAD CoE components, like the NOMAD
Encyclopedia and NOMAD Analytics Toolkit, to fully integrate NOMAD with one GUI and consistent
APIs. Furthermore, this projects aims at establishing NOMAD as a distributed platform for
13
14
15
16
17
18
material science data sharing and management. This includes the on-site deployment of
NOMAD as a standalone service (*oasis*), the federated use of NOMAD through a
serious of full and partial *mirrors*, the integration of 3rd party material science
databases (i.e. [Aflow](http://www.aflow.org/), [OQMD](http://oqmd.org/),
[Materials Project](https://materialsproject.org/)), and support for open APIs and
standards like the [Optimade](http://www.optimade.org/) API.
19

20

21
## Getting started
22

Markus Scheidgen's avatar
Markus Scheidgen committed
23
24
25
26
27
28
### Using NOMAD as a Python package

You can install the `nomad` Python package from source distribution with pip. Please
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.
```
29
pip install nomad-lab
Markus Scheidgen's avatar
Markus Scheidgen committed
30
31
32
33
```

To **use the NOMAD parsers for example**, install the `parsing` extra:
```
34
pip install nomad-lab[parsing]
Markus Scheidgen's avatar
Markus Scheidgen committed
35
nomad parse --show-archive <your-file-to-parse>
Markus Scheidgen's avatar
Markus Scheidgen committed
36
37
38
39
```

### For NOMAD developer

40
Read the [docs](https://nomad-lab.eu/prod/rae/docs/index.html). The documentation is also part
41
42
of the source code. It covers aspects like introduction, architecture, development setup/deployment,
contributing, and API reference.
43

Markus Scheidgen's avatar
Markus Scheidgen committed
44
45

## Change log
46

Markus Scheidgen's avatar
Markus Scheidgen committed
47
Omitted versions are plain bugfix releases with only minor changes and fixes.
Markus Scheidgen's avatar
Markus Scheidgen committed
48

49
50
### v0.9.8
- A new library for parsing text-based raw files.
Markus Scheidgen's avatar
Markus Scheidgen committed
51
52
- A new main menu in the GUI.
- Updated documentation.
53

Markus Scheidgen's avatar
Markus Scheidgen committed
54
55
56
### v0.9.3
- Encyclopedia with dedicated materials search index.

57
### v0.9.0
58
59
60
61
62
63
64
65
66
67
- The encyclopedia runs on top of the new infrastructure. The GUIs are integrated via
  bi-lateral navigation between entries.
- The parsers have new documentation and development instructions and can be easily developed
  based on NOMAD's PyPi package nomad-lab
- We introduce workflow metadata (starting with geometry optimizations). This includes search
  for workflow parameter, and 3-tiered archive storage for quick access to results for analytics.
- A new GUI to browse  the Archive and Metainfo
- The Artificial Intelligence Toolkit (at least its tutorial page) is part of the GUI
- The OASIS comprises Repository, Archive, Metainfo, Encyclopedia, and Artificial Intelligence Toolkit.

68
69
70
### v0.8.7
- a new variant of the Metainfo browser

Markus Scheidgen's avatar
Markus Scheidgen committed
71
72
### v0.8.1
- switched to support Python 3.7
73
- client library as pypi package `nomad-lab`
Markus Scheidgen's avatar
Markus Scheidgen committed
74

75
76
### v0.8.0
- new underlying datamodel that allows to maintain multiple domains
Markus Scheidgen's avatar
Markus Scheidgen committed
77
- multiple domains supported the GUI
78
- new metainfo implementation
79
- API endpoint to access the metainfo
80
81
82
83
- new archive based on new metainfo
- client library that serves archive data as objects (with tab completion) not dictionaries
- properties and user tab in the search GUI
- improved performance on most parsers
Markus Scheidgen's avatar
Markus Scheidgen committed
84
- NOMAD source distribution
85

86
87
88
89
### v0.7.9
- Everything to run a simple NOMAD OASIS based on the central user-management
- minor bugfixes

90
91
92
93
### v0.7.7
- Shows dataset contents with embargo data, but hides the entry details (raw-files, archive)
- minor bugfixes

94
### v0.7.5
Markus Scheidgen's avatar
Markus Scheidgen committed
95
- AFLOWLIB prototypes (archive)
96
97
- primitive label search
- improved search performance based on excluded fields
Markus Scheidgen's avatar
Markus Scheidgen committed
98
- improved logs
99
100
- minor bugfixes

101
102
103
104
105
106
107
108
### v0.7.3
- fixed aborted raw-file downloads
- improved representation of data availability (staging, embargo, public) in GUI
- user data uploads ordered by upload time
- user data shows uploads with name
- configurable embargo period length
- minor bugfixes

109
110
111
112
### v0.7.2
- API curl, Python, and results for entries and search queries shown in the GUI
- minor bugfixes

Markus Scheidgen's avatar
Markus Scheidgen committed
113
114
115
116
### v0.7.1
- Download of archive files based on search queries
- minor bugfixes

Markus Scheidgen's avatar
Markus Scheidgen committed
117
### v0.7.0
118
119
- User metadata editing and datasets with DOIs
- Revised GUI lists (entries, grouped entries, datasets, uploads)
120
- Keycloak based user management
121
122
- Rawfile preview
- no dependencies with the old NOMAD CoE Repository
123
124
125
126
127
128
129

### v0.6.2
- GUI performance enhancements
- API /raw/query endpoint takes file pattern to further filter download contents and
  strips potential shared path prefixes for a cleaner download .zip
- Stipped common path prefixes in raw file downloads
- minor bugfixes
130

131
### v0.6.0
Markus Scheidgen's avatar
Markus Scheidgen committed
132
- GUI URL, and API endpoint that resolves NOMAD CoE legacy PIDs
133
134
- Support for datasets in the GUI
- more flexible search python module and repo API
Markus Scheidgen's avatar
Markus Scheidgen committed
135
- support for external_id
136
- support for code-based raw_id
137
- Optimade API 0.10.0
138
- GUI supports Optimade filter query and other quantities
139
140
- minor bugfixes

141
142
143
144
145
### v0.5.2
- allows to download large files over longer time period
- streamlined deployment without API+GUI proxy
- minor bugfixes

Markus Scheidgen's avatar
Markus Scheidgen committed
146
### v0.5.1
Markus Scheidgen's avatar
Markus Scheidgen committed
147
- integrated parsers Dmol3, qbox, molcas, fleur, and onetep
148
- API endpoint for query based raw file download
Markus Scheidgen's avatar
Markus Scheidgen committed
149
- improvements to admin cli: e.g. clean staging files, reprocess uploads based on codes
150
- improved error handling in the GUI
Markus Scheidgen's avatar
Markus Scheidgen committed
151
- lots of parser bugfixes
Markus Scheidgen's avatar
Markus Scheidgen committed
152
153
- lots of minor bugfixes

154
### v0.5.0
155
156
The first production version of nomad@fairdi as the upload API and gui for NOMAD
- Production ready software and deployments (term agreements, better GUI docs)
157
158
159
- Raw file API with support to list directories. This replaces the `files` calculation
  metadata key. It was necessary due to arbitrary large lists of *auxfiles* in some
  calculations.
160
- Search interface that contains all features of the CoE Repository GUI.
161
162
163
- Refactored search API that allows to search for entries (paginated + scroll),
  metrics based on quantity aggregations (+ paginated entries), quantity aggregations
  with all values via `after` key (+ paginated entries).
164
165
166
- reprocessing of published results (e.g. after parser/normalizer improvements)
- mirror functionality
- refactored command line interface (CLI)
167
- potential GUI user tracking capabilities
168
- many minor bugfixes
169

170
171
172
173
### v0.4.7
- more migration scripts
- minor bugfixes

174
175
176
177
178
179
### v0.4.6
- admin commands to directly manipulate upload data
- additional migration scripts
- fixed system normalizer to understand indexed atom labels correctly
- many minor bugfixes

180
181
182
183
184
### v0.4.5
- improved uploads view with published uploads
- support for publishing to the existing nomad CoE repository
- many minor bugfixes

185
### v0.4.4
186
- improved GUI navigation
187
188
- support for multiple domains
- info API endpoint
Markus Scheidgen's avatar
Markus Scheidgen committed
189
- metainfo browser
Markus Scheidgen's avatar
Markus Scheidgen committed
190
- support for latest exciting version
Markus Scheidgen's avatar
Markus Scheidgen committed
191
- bugfixes in system normalization
Markus Scheidgen's avatar
Markus Scheidgen committed
192
- many minor bugfixes
193

194
195
196
197
198
199
200
### v0.4.3
- more flexible celery routing
- config via nomad.yml
- repo_db can be disabled
- publishing of calculations with failed processing
- cli for managing running processing tasks

Markus Scheidgen's avatar
Markus Scheidgen committed
201
202
203
### v0.4.2
- bugfixes regarding the migration
- better migration configurability and reproducibility
Markus Scheidgen's avatar
Markus Scheidgen committed
204
- scales to multi node kubernetes deployment