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11 Commits

Author SHA1 Message Date
Jethro Kuan
6170cc9928 (release): bump 2021 -> 2022, 2.1.0 -> 2.2.0 2022-01-14 10:53:56 -08:00
Jethro Kuan
cc95540135 (fix): hotfix changelog 2022-01-14 10:51:06 -08:00
Jethro Kuan
24a683d58c (release): 2.2.0 (#2037) 2022-01-14 10:50:21 -08:00
Nicolas Chachereau
86c9085363 (fix)core: make 'fd and 'fdfind backend work for listing files (#2021) 2022-01-11 15:05:27 -08:00
Andrey Akulov
b67bccd6c2 (feat)dailies: add keys argument to org-roam-dailies-capture-today and org-roam-dailies--capture (#2028) 2022-01-11 14:13:40 -08:00
Jethro Kuan
8b43093d1a (fix)org-roam-with-file: ensure local variables are respected (#2033)
When visiting a file, ensure that local variables are respected.
2022-01-12 03:38:44 +08:00
Noboru Ota
679ef6ef00 (fix)db: pragma foreign keys to work with sqlite3 (#2018)
* (fix):db: pragma foreign keys to work with sqlite3

This commit is follow-up for PR #2009 should fix issues #1927 & #1910.

Currently, `[:pragma (= foreign_keys ON)]` is present only in function
`org-roam-db--init`. This means the `foreign_keys` is turned on only when the db
file is created for the first time. Subsequent Emacs sessions won't turn it on
as the db file is already present and does not evaluate `org-roam-db--init`.

This PRAGMA needs to be turned on each database connection at runtime according
to sqlite's documentation (https://sqlite.org/foreignkeys.html#fk_enable)

```
Foreign key constraints are disabled by default (for backwards compatibility),
so must be enabled separately for each database connection
```

I have observed that on Windows only the Emacs session that initially creates
the Org-roam db file works correctly with the `sqlite3` option. Subsequent Emacs
sessions have the same "Unique constraint failed" error messages.

I have tested this patch on Windows and Ubuntu; both seem to work in the first
and subsequent Emacs sessions.

I am not 100% sure if the location of the PRAGMA is the best; use it as a
proof-of-cocenpt for the fix. Thank you.

* remove: [:pragma (= foreign_keys ON)] from org-roam-db--init

* fix: defconst org-roam--sqlite-available-p outputs error

When `org-roam-database-connector` is not `sqlite`, it outputs an unnecessary
error when Org-roam starts up as `defconst` evaluates
`(emacsql-sqlite-ensure-binary)`.

```
Org-roam initialization: (error "No EmacSQL SQLite binary available, aborting")
```

For other database connectors, this is not relevant.

* chore: rm org-roam--sqlite-available-p

As per our conversation, org-roam--sqlite-available-p not needed.
2022-01-02 14:03:30 +08:00
Bruce D'Arcus
ee9a8d423e doc: Add mention of org-cite to bibliography (#2015)
* doc: Add mention of org-cite to bibliography

* regenerate texi

Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>
2021-12-27 18:07:27 +08:00
Jethro Kuan
d3c7d74329 (feat)db: allow [cite:@foo] links in ROAM_REFS (#2017) 2021-12-27 16:05:17 +08:00
lorniu
3bf0a0a35d Use locate-user-emacs-file instead of expand-file-name. (#2016)
Then all advices on `locate-user-emacs-file` will work.
2021-12-27 14:37:46 +08:00
Noboru Ota
d0f17c6477 (docs): correct how to install gcc on Windows (#2013)
* docs: Correct how to install gcc on Windows

PATH needs to be manually set on Windows. Previously, it was explicitly
mentioned that it was unnecessary. More recent experience is that it's necessary.

* regenerate texi

Co-authored-by: Jethro Kuan <jethrokuan95@gmail.com>
2021-12-23 17:22:02 +08:00
15 changed files with 97 additions and 40 deletions

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@@ -1,8 +1,12 @@
# Changelog
## TBD
## 2.2.0
### Added
- [#1806](https://github.com/org-roam/org-roam/pull/1806) db: support caching and usage of Org 9.5's in-built citations
- [#1806](https://github.com/org-roam/org-roam/pull/1806), [#2017](https://github.com/org-roam/org-roam/pull/2017) db: support caching and usage of Org 9.5's in-built citations
- [#1963](https://github.com/org-roam/org-roam/pull/1963) db: cache file title into files table
- [#1977](https://github.com/org-roam/org-roam/pull/1977) db: support Org-ref v3 citations
- [#1907](https://github.com/org-roam/org-roam/pull/1907), [#2009](https://github.com/org-roam/org-roam/pull/2009), [#2018](https://github.com/org-roam/org-roam/pull/2018) db: support sqlite3
- [#2028](https://github.com/org-roam/org-roam/pull/2028) dailies: add `keys` argument to `org-roam-dailies-capture-today` and `org-roam-dailies--capture` functions to give the abilty to get into a capture buffer bypassing the selection screen
### Removed
### Changed
@@ -10,12 +14,22 @@
- [#1809](https://github.com/org-roam/org-roam/pull/1809) capture: the mandatory `:if-new` property of each capture template is now renamed to `:target`
- [#1829](https://github.com/org-roam/org-roam/pull/1829) perf: file sql updates are now wrapped in a transaction
- [#1877](https://github.com/org-roam/org-roam/pull/1877) dailies: stop asking for time, only date
- [#1949](https://github.com/org-roam/org-roam/pull/1949) db: check for property drawers are now case-insensitive
### Fixed
- [#1798](https://github.com/org-roam/org-roam/pull/1798) org-roam-node-at-point: do not skip invisible headings
- [#1807](https://github.com/org-roam/org-roam/pull/1807) capture: always trigger `:if-new` template for existing nodes
- [#1813](https://github.com/org-roam/org-roam/pull/1813) db: prevent empty ROAM_ALIASES from crashing db updates
- [#1816](https://github.com/org-roam/org-roam/pull/1816) db: prevent invalid ROAM_REFS from crashing db updates
- [#1893](https://github.com/org-roam/org-roam/pull/1893), [#1896](https://github.com/org-roam/org-roam/pull/1896), [#1901](https://github.com/org-roam/org-roam/pull/1901), [#1895](https://github.com/org-roam/org-roam/pull/1895), [#1904](https://github.com/org-roam/org-roam/pull/1904) completions: various mini-buffer related completion fixes
- [#1931](https://github.com/org-roam/org-roam/pull/1931) utils: org-roam-set-keyword now skips over all drawers
- [#1947](https://github.com/org-roam/org-roam/pull/1947) db: links in ROAM_REFS are no longer considered as links
- [#1948](https://github.com/org-roam/org-roam/pull/1948) completions: fix same-line completions
- [#1953](https://github.com/org-roam/org-roam/pull/1953) db: refresh CATEGORY before writing to db
- [#1946](https://github.com/org-roam/org-roam/pull/1946), [#1946](https://github.com/org-roam/org-roam/pull/1946), [#1958](https://github.com/org-roam/org-roam/pull/1958) various performance improvements
- [#1980](https://github.com/org-roam/org-roam/pull/1980) utils: fix org-roam-with-file changing the minor-mode
- [#2016](https://github.com/org-roam/org-roam/pull/2016) db: fix node caching being affected by agenda variables
- [#2033](https://github.com/org-roam/org-roam/pull/2023) db: respect local variables during db parsing
## 2.1.0
### Added

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@@ -1,20 +1,20 @@
#+title: Org-roam User Manual
#+author: Jethro Kuan
#+email: jethrokuan95@gmail.com
#+date: 2020-2021
#+date: 2020-2022
#+language: en
#+texinfo_deffn: t
#+texinfo_dir_category: Emacs
#+texinfo_dir_title: Org-roam: (org-roam).
#+texinfo_dir_desc: Roam Research for Emacs.
#+subtitle: for version 2.1.0
#+subtitle: for version 2.2.0
#+options: H:4 num:3 toc:nil creator:t ':t
#+property: header-args :eval never
#+texinfo: @noindent
This manual is for Org-roam version 2.1.0.
This manual is for Org-roam version 2.2.0.
#+BEGIN_QUOTE
Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
@@ -711,6 +711,16 @@ citation key:
:END:
#+end_src
or
#+begin_src org
,* Probabilistic Robotics
:PROPERTIES:
:ID: 51b7b82c-bbb4-4822-875a-ed548cffda10
:ROAM_REFS: [cite:@thrun2005probabilistic]
:END:
#+end_src
for ~org-cite~, or:
#+begin_src org
@@ -1351,6 +1361,9 @@ documents (PDF, EPUB etc.) within Org-mode.
** Bibliography
Org 9.5 added native citation and bibliography functionality, called "org-cite",
which org-roam supports.
[[https://github.com/org-roam/org-roam-bibtex][org-roam-bibtex]] offers tight integration between [[https://github.com/jkitchin/org-ref][org-ref]], [[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] and
~org-roam~. This helps you manage your bibliographic notes under ~org-roam~.

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@@ -31,7 +31,7 @@ General Public License for more details.
@finalout
@titlepage
@title Org-roam User Manual
@subtitle for version 2.1.0
@subtitle for version 2.2.0
@author Jethro Kuan
@page
@vskip 0pt plus 1filll
@@ -44,7 +44,7 @@ General Public License for more details.
@noindent
This manual is for Org-roam version 2.1.0.
This manual is for Org-roam version 2.2.0.
@quotation
Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@@gmail.com>
@@ -1066,7 +1066,7 @@ Remove a ref from the node at point.
Since version 9.5, Org has first-class support for citations. Org-roam supports
the caching of both these in-built citations (of form @code{[cite:@@key]}) and @uref{https://github.com/jkitchin/org-ref, org-ref}
citations (of form @uref{key}).
citations (of form cite:key).
Org-roam attempts to load both the @code{org-ref} and @code{org-cite} package when
indexing files, so no further setup from the user is required for citation
@@ -1091,6 +1091,16 @@ citation key:
:END:
@end example
or
@example
* Probabilistic Robotics
:PROPERTIES:
:ID: 51b7b82c-bbb4-4822-875a-ed548cffda10
:ROAM_REFS: [cite:@@thrun2005probabilistic]
:END:
@end example
for @code{org-cite}, or:
@example
@@ -1896,6 +1906,9 @@ documents (PDF, EPUB etc.) within Org-mode.
@node Bibliography
@section Bibliography
Org 9.5 added native citation and bibliography functionality, called ``org-cite'',
which org-roam supports.
@uref{https://github.com/org-roam/org-roam-bibtex, org-roam-bibtex} offers tight integration between @uref{https://github.com/jkitchin/org-ref, org-ref}, @uref{https://github.com/tmalsburg/helm-bibtex, helm-bibtex} and
@code{org-roam}. This helps you manage your bibliographic notes under @code{org-roam}.

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@@ -7,7 +7,7 @@
;; Leo Vivier <leo.vivier+dev@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org-roam "2.1"))
;; This file is NOT part of GNU Emacs.
@@ -130,11 +130,14 @@ See `org-roam-capture-templates' for the template documentation."
;;; Commands
;;;; Today
;;;###autoload
(defun org-roam-dailies-capture-today (&optional goto)
(defun org-roam-dailies-capture-today (&optional goto keys)
"Create an entry in the daily-note for today.
When GOTO is non-nil, go the note without creating an entry."
When GOTO is non-nil, go the note without creating an entry.
ELisp programs can set KEYS to a string associated with a template.
In this case, interactive selection will be bypassed."
(interactive "P")
(org-roam-dailies--capture (current-time) goto))
(org-roam-dailies--capture (current-time) goto keys))
;;;###autoload
(defun org-roam-dailies-goto-today ()
@@ -300,11 +303,15 @@ Return (MONTH DAY YEAR) or nil if not an Org time-string."
;;; Capture implementation
(add-to-list 'org-roam-capture--template-keywords :override-default-time)
(defun org-roam-dailies--capture (time &optional goto)
(defun org-roam-dailies--capture (time &optional goto keys)
"Capture an entry in a daily-note for TIME, creating it if necessary.
When GOTO is non-nil, go the note without creating an entry."
When GOTO is non-nil, go the note without creating an entry.
ELisp programs can set KEYS to a string associated with a template.
In this case, interactive selection will be bypassed."
(let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
(org-roam-capture- :goto (when goto '(4))
:keys keys
:node (org-roam-node-create)
:templates org-roam-dailies-capture-templates
:props (list :override-default-time time)))

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@@ -5,7 +5,7 @@
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
;; This file is NOT part of GNU Emacs.

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@@ -5,7 +5,7 @@
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
;; This file is NOT part of GNU Emacs.

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@@ -4,7 +4,7 @@
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
;; This file is NOT part of GNU Emacs.

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@@ -5,7 +5,7 @@
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
;; This file is NOT part of GNU Emacs.

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@@ -5,7 +5,7 @@
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1"))
;; This file is NOT part of GNU Emacs.

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@@ -5,7 +5,7 @@
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
;; This file is NOT part of GNU Emacs.
@@ -54,7 +54,7 @@ a compiler. See https://nullprogram.com/blog/2014/02/06/."
(const sqlite3)
(symbol :tag "other")))
(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
(defcustom org-roam-db-location (locate-user-emacs-file "org-roam.db")
"The path to file where the Org-roam database is stored.
It is the user's responsibility to set this correctly, especially
@@ -101,12 +101,6 @@ slow."
;;; Variables
(defconst org-roam-db-version 18)
;; TODO Rename this
(defconst org-roam--sqlite-available-p
(with-demoted-errors "Org-roam initialization: %S"
(emacsql-sqlite-ensure-binary)
t))
(defvar org-roam-db--connection (make-hash-table :test #'equal)
"Database connection to Org-roam database.")
@@ -145,6 +139,7 @@ Performs a database upgrade when required."
(let ((init-db (not (file-exists-p org-roam-db-location))))
(make-directory (file-name-directory org-roam-db-location) t)
(let ((conn (funcall (org-roam-db--conn-fn) org-roam-db-location)))
(emacsql conn [:pragma (= foreign_keys ON)])
(when-let ((process (emacsql-process conn)))
(set-process-query-on-exit-flag process nil))
(puthash (expand-file-name (file-name-as-directory org-roam-directory))
@@ -243,7 +238,6 @@ The query is expected to be able to fail, in this situation, run HANDLER."
(defun org-roam-db--init (db)
"Initialize database DB with the correct schema and user version."
(emacsql db [:pragma (= foreign_keys ON)])
(emacsql-with-transaction db
(pcase-dolist (`(,table ,schema) org-roam-db--table-schemata)
(emacsql db [:create-table $i1 $S2] table schema))
@@ -482,9 +476,24 @@ INFO is the org-element parsed buffer."
(let (rows)
(dolist (ref refs)
(save-match-data
(cond ((string-prefix-p "@" ref)
(cond (;; @citeKey
(string-prefix-p "@" ref)
(push (vector node-id (substring ref 1) "cite") rows))
((string-match org-link-plain-re ref)
(;; [cite:@citeKey]
(string-prefix-p "[cite:" ref)
(condition-case nil
(let ((cite-obj (org-cite-parse-objects ref)))
(org-element-map cite-obj 'citation-reference
(lambda (cite)
(let ((key (org-element-property :key cite)))
(push (vector node-id key "cite") rows)))))
(error
(lwarn '(org-roam) :warning
"%s:%s\tInvalid cite %s, skipping..." (buffer-file-name) (point) ref))))
(;; https://google.com, cite:citeKey
;; Note: we use string-match here because it matches any link: e.g. [[cite:abc][abc]]
;; But this form of matching is loose, and can accept invalid links e.g. [[cite:abc]
(string-match org-link-plain-re ref)
(let ((link-type (match-string 1 ref))
(path (match-string 2 ref)))
(if (and (boundp 'org-ref-cite-types)

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@@ -5,7 +5,7 @@
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
;; This file is NOT part of GNU Emacs.

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@@ -1,11 +1,11 @@
;;; org-roam-mode.el --- Major mode for special Org-roam buffers -*- lexical-binding: t -*-
;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
;; This file is NOT part of GNU Emacs.

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@@ -5,7 +5,7 @@
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (magit-section "3.0.0"))
;; This file is NOT part of GNU Emacs.

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@@ -1,11 +1,11 @@
;;; org-roam-utils.el --- Utilities for Org-roam -*- lexical-binding: t; -*-
;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4"))
;; This file is NOT part of GNU Emacs.
@@ -119,7 +119,8 @@ Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
(delay-mode-hooks
(let ((org-inhibit-startup t)
(org-agenda-files nil))
(org-mode))))
(org-mode)
(hack-local-variables))))
(setq res (progn ,@body))
(unless (and new-buf (not ,keep-buf-p))
(save-buffer)))

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@@ -5,7 +5,7 @@
;; Author: Jethro Kuan <jethrokuan95@gmail.com>
;; URL: https://github.com/org-roam/org-roam
;; Keywords: org-mode, roam, convenience
;; Version: 2.1.0
;; Version: 2.2.0
;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
;; This file is NOT part of GNU Emacs.
@@ -279,8 +279,8 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
(defun org-roam--list-files-fd (executable dir)
"Return all Org-roam files under DIR, using \"fd\", provided as EXECUTABLE."
(let* ((globs (org-roam--list-files-search-globs org-roam-file-extensions))
(extensions (string-join (mapcar (lambda (glob) (substring glob 2 -1)) globs) " -e "))
(command (string-join `(,executable "-L" ,dir "--type file" ,extensions) " ")))
(extensions (string-join (mapcar (lambda (glob) (concat "-e " (substring glob 2 -1))) globs) " "))
(command (string-join `(,executable "-L" "--type file" ,extensions "." ,dir) " ")))
(org-roam--shell-command-files command)))
(defalias 'org-roam--list-files-fdfind #'org-roam--list-files-fd)