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@@ -13,5 +13,3 @@ RUN python setup.py develop
 #CMD ["/bin/bash"]
 CMD [ "python", "abcd/server/__init__.py" ]
 #CMD ["gunicorn", "-w 4", "-b 0.0.0.0:8000", "server:app"]
-
-

README.md

@@ -3,17 +3,17 @@
 [![Doc](https://img.shields.io/badge/docs-master-green.svg)](https://libatoms.github.io/abcd/)
 [![Build Status](https://travis-ci.org/libAtoms/abcd.svg?branch=master)](https://travis-ci.org/libAtoms/abcd)
 
-Database storage and discovery of atomistic data. 
+Database storage and discovery of atomistic data.
 
 Take a look at the `examples.md` file for.. examples!
 
 Main features:
 
-- Configurations that consist of atom positions, elements, forces, and various metadata are stored as a dictionary by a MongoDB backend. 
-- There is no predefined schema, any combination of keys are allowed for all configurations. 
-- Two modes: "discovery" and "download". Both use filter-type queries, but in "discovery" mode, summary statistics of the configurations that pass the filter are reported. In "download" mode, the matching configurations are downloaded and exported to a file. 
-- The "discovery" mode can be used to learn what keys exist in the set of configurations that have passed the current quiery filter. The user can use this to refine the query. 
-- Complex queries on dictionary key-value pairs are allowed, and their logical combinations. 
+- Configurations that consist of atom positions, elements, forces, and various metadata are stored as a dictionary by a MongoDB backend.
+- There is no predefined schema, any combination of keys are allowed for all configurations.
+- Two modes: "discovery" and "download". Both use filter-type queries, but in "discovery" mode, summary statistics of the configurations that pass the filter are reported. In "download" mode, the matching configurations are downloaded and exported to a file.
+- The "discovery" mode can be used to learn what keys exist in the set of configurations that have passed the current quiery filter. The user can use this to refine the query.
+- Complex queries on dictionary key-value pairs are allowed, and their logical combinations.
 
 ## Installation
 
@@ -24,13 +24,13 @@ $ pip install git+https://github.com/libAtoms/abcd.git
 
 ## Setup
 
-If you have an already running mongo server, or install your own, they you are ready to go. Alternatively, 
+If you have an already running mongo server, or install your own, they you are ready to go. Alternatively,
 
 ```
 docker run -d --rm --name abcd-mongodb -v <path-on-your-machine-to-store-database>:/data/db -p 27017:27017 mongo
 ```
 
-will download and install a docker and run a database in it. 
+will download and install a docker and run a database in it.
 
 To connect to a mongodb that is already running, use
 ```
@@ -56,7 +56,7 @@ You can set up an `abcd` user on your machine where the database is running, and
 command="/path/to/abcd --remote  ${SSH_ORIGINAL_COMMAND}",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty ssh-rsa <public-key> your@email
 ```
 
-Then you'll be able to access the database remotely using, e.g. 
+Then you'll be able to access the database remotely using, e.g.
 ```
 ssh [email protected] summary
 ```
@@ -74,18 +74,18 @@ To access it:
     docker pull stenczelt/projection-abcd:latest
     ```
 
-2. create a docker network, which enables the containers to communicate with each other and the outside world as well 
+2. create a docker network, which enables the containers to communicate with each other and the outside world as well
     ```
     docker network create --driver bridge abcd-network
     ```
 
 3. run the mongo (ABCD) and the visualiser as well
     ```
     docker run -d --rm --name abcd-mongodb-net -v <path-on-your-machine-to-store-database>:/data/db -p 27017:27017 --network abcd-network mongo
-    
+
     docker run -it --rm --name visualiser-dev -p 9999:9999 --network abcd-network stenczelt/projection-abcd
     ```
-    NB: You need a a directory where the database files are kept locally and you need to connect this to the mongo 
+    NB: You need a a directory where the database files are kept locally and you need to connect this to the mongo
     container. More info about this can be found in the original ABCD repo
 
 This will start the visualiser with ABCD integration! Have fun!

abcd/parsers/extras.py

@@ -10,24 +10,24 @@
 
     NAME: ("_"|LETTER|DIGIT) ("_"|"-"|LETTER|DIGIT)*
 
-    ?value: 
+    ?value:
           | ESCAPED_STRING     -> string
           | integer
           | float
           | boolean
           | WORD
           | "null"             -> null
-          
+
     arrays: "[" value (","? value)* "]"
           | "{" value (","? value)* "}"
           | "(" value (","? value)* ")"
-    
-    ?integer: INT -> int 
+
+    ?integer: INT -> int
             | array_int
-    
-    ?float: FLOAT -> float 
+
+    ?float: FLOAT -> float
           | array_float
-    
+
     ?boolean: true | false | array_boolean
 
     true: "T" | "true"
@@ -36,20 +36,20 @@
     array_int: "[" integer ([","] integer)* "]"
              | "{" integer ([","] integer)* "}"
              | "(" integer ([","] integer)* ")"
-             
-    
+
+
     array_float: "[" float ([","] float)* "]"
                | "{" float ([","] float)* "}"
                | "(" float ([","] float)* ")"
 
     array_boolean: "[" boolean ([","] boolean)* "]"
                | "{" boolean ([","] boolean)* "}"
                | "(" boolean ([","] boolean)* ")"
-    
-    
-    INT.3: SIGNED_INT 
+
+
+    INT.3: SIGNED_INT
     FLOAT.4: SIGNED_FLOAT
-          
+
     %import common.ESCAPED_STRING
     %import common.LETTER
     %import common.WORD

abcd/parsers/queries.py

@@ -12,13 +12,13 @@
     ?statement:                                   -> empty
               | expression                        -> single_statement
               | statement relation_ops expression -> multi_statement
-    
-    ?expression: NAME                      -> single_expression 
-               | NAME comparison_ops value -> operator_expression 
-               | value reversed_ops NAME   -> reversed_expression 
-               | "(" statement ")"         -> grouped_expression 
+
+    ?expression: NAME                      -> single_expression
+               | NAME comparison_ops value -> operator_expression
+               | value reversed_ops NAME   -> reversed_expression
+               | "(" statement ")"         -> grouped_expression
                | NOT statement             -> negation_expression
-        
+
     ?comparison_ops: EQ
               | NEQ
               | RE
@@ -27,21 +27,21 @@
               | LT
               | LTE
 
-    ?relation_ops: AND 
-                 | OR 
+    ?relation_ops: AND
+                 | OR
 
     AND: "&&" | "and"
     OR:  "||" | "or"
     NOT: "!" | "not"
 
     ?reversed_ops: IN
-        
-    EQ:   "=" 
-    NEQ:  "!=" 
-    RE:    "~"     
-    GT:   ">" 
-    GTE:  ">=" 
-    LT:   "<" 
+
+    EQ:   "="
+    NEQ:  "!="
+    RE:    "~"
+    GT:   ">"
+    GTE:  ">="
+    LT:   "<"
     LTE:  "<="
     IN:    "in"
 
@@ -54,26 +54,26 @@
          | array
 
     array: "[" value ([","] value)* "]"
-    
+
     //function: all | any
-    
-    //all: "all" "(" NAME ")" 
+
+    //all: "all" "(" NAME ")"
     //any: "any" "(" NAME ")"
 
     //NAME : /(?!and\b)/ /(?!or\b)/ /(?!not\b)/ CNAME
 
     // Strings
     _STRING_INNER: /.*?/
-    _STRING_ESC_INNER: _STRING_INNER /(?<!\\)(\\\\)*?/ 
-    
+    _STRING_ESC_INNER: _STRING_INNER /(?<!\\)(\\\\)*?/
+
     STRING : "\"" _STRING_ESC_INNER "\""
            | "'" _STRING_ESC_INNER "'"
 
-    NAME: ("_"|LETTER|DIGIT) ("_"|"-"|LETTER|DIGIT)*  
+    NAME: ("_"|LETTER|DIGIT) ("_"|"-"|LETTER|DIGIT)*
 
     %import common.LETTER
     %import common.DIGIT
-    
+
     %import common.SIGNED_FLOAT   -> FLOAT
     %import common.SIGNED_INT     -> INT
     %import common.WS_INLINE

abcd/server/app/templates/database/database.html

@@ -75,4 +75,3 @@
     </div>
 
 {%- endblock %}
-

abcd/server/app/templates/login.html

@@ -41,4 +41,3 @@ <h1 class="h3 mb-3 font-weight-normal">Sign in</h1>
 
 
 {%- endblock %}
-

abcd/test.xyz

@@ -1,4 +1,4 @@
 2
 Properties=species:S:1:pos:R:3 s="string value" _vtk_test="t e s t _ s t r" pbc="F F F"
 Si       0.00000000       0.00000000       0.00000000
-Si       0.00000000       0.00000000       0.00000000
+Si       0.00000000       0.00000000       0.00000000

docker-compose.yml

@@ -39,4 +39,4 @@ services:
       - ME_CONFIG_MONGODB_ADMINUSERNAME=${DB_USER}
       - ME_CONFIG_MONGODB_ADMINPASSWORD=${DB_PASS}
     depends_on:
-      - mongo
+      - mongo

docs_src/Makefile

@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs_src/install.rst

@@ -11,4 +11,3 @@ Local installation
 
 Installation with remote access
 -------------------------------
-

docs_src/usage.rst

@@ -8,7 +8,3 @@ Command line tool
 
 Python interface
 ----------------
-
-
-
-

examples.md

@@ -10,7 +10,7 @@ abcd upload -e cas VelocityVerlet_flexible_step0.5.xyz
 abcd upload -e cas silicon_database_gp_iter6_sparse9k.xml.xyz
 # get around the silly calculator/atoms object storage nightmare of ASE:
 # the -i option tells ABCD to ignore the fake ASE calculator that gets created when xyz files are imported
-abcd upload -i -e cas Ti_N54_database.xyz 
+abcd upload -i -e cas Ti_N54_database.xyz
 ```
 The most often used command is `summary`, it tells you how many configurations match a query. Together with the `-p` option, it gives histograms of those properties.
 ```
@@ -24,7 +24,7 @@ abcd summary -q 'formula="H250O125"' -q cas -p formula
 # regular expressions! the `~` operator does RegExp matching
 abcd summary -q 'formula~"H.*O.*"' -q cas -p formula
 ```
-Note how all strings need to be quoted, and those quotes protected from the shell. 
+Note how all strings need to be quoted, and those quotes protected from the shell.
 
 ```
 abcd rename-key --help